Stokes is unavailable for the current Ashes series in Australia as he still waits to hear whether the Crown Prosecution Service advises police to charge him or not following his arrest on suspicion of causing actual bodily harm.
But the England all-rounder is playing again, for Canterbury Kings in New Zealand’s Ford Trophy competition, and Morgan believes that is a wise move as Stokes waits on the decision over the late-night fracas in Bristol in September.
Alex Hales will face no criminal charges over the same Bristol incident and can expect to be selected when England announce their squad for the limited-overs leg of their Australia trip on Wednesday night.
Morgan said: “Alex is definitely clear to play and regarding Ben, we are still waiting to see what happens.
“He is obviously getting cricket under his belt which is a really good decision.
“He has started to hit balls this week and there is only so much you can get indoor, banging bowling machine balls.
“But for him as an all-rounder to get miles under his leg as a bowler – given that he could potentially come back quickly – personally to look after his own body is a good decision.”
Stokes again struggled to make an impact for Canterbury after scoring just two and going wicketless on his debut on Sunday.
He made 34 from 41 balls and failed to take a scalp as Canterbury fell to a seven-wicket defeat to Auckland on Wednesday.
Asked whether Stokes would be available for the start of the ODI series in Australia on January 14, Morgan replied: “We just don’t know and I don’t think anybody does.
“There is an investigation going on and it is in the hands of police.
“But it is going to be a really exciting series. Australia is a tough place to tour no matter what format you are playing in and given where we are at with 50-over cricket it is a great time to tour there.
“It is a good time to expose some of our mistakes.
“I would rather know what they are now and try to fix it rather than having a free run for quite a while and then have to rectify anything at the last minute ahead of the World Cup.”
Morgan has become a one-day specialist for England in recent times, both in 50-over and Twenty20 cricket.
The 31-year-old Irishman played the last of his 16 Tests nearly six years ago and he does not expect to represent England in the long format of the game again.
“I don’t see me playing Test cricket ever again,” Morgan said.
“My focus is solely on the 2019 World Cup and everything is being driven into that at the moment.
“It is nice you don’t have to chop and change in between formats.
“I would obviously love to play Test match cricket but that is never going to happen.”
*Eoin Morgan was speaking on behalf of Royal London as they marked two more years of sponsorship of one-day cricket.
Joe Root’s side came into the final day of the second Test needing another 178 runs to win but they lost six wickets for just 64 runs.
Now they head to Perth – a traditional stronghold for Australia – knowing another defeat would see them lose the urn.
The former England captain doubts the current crop has what it takes to turn the series around.
“We have mentioned the whitewash and you have to,” Vaughan told BT Sport.
“At the minute you are looking at this team, can you get 20 wickets? I would say I would doubt it. Can they get enough runs to put Australia under enough pressure to win the Test match? From the first two games I very much doubt it.
“I hate to be the gloom and doom merchant but it doesn’t look good.
“You look at the scores, they have had good conditions to bat. For England to win Test matches you have to get bigger scores, individual players have to get hundreds.
“You’re looking at the England side, can they get big scores? You have to say from what we have seen in the four innings that it is going to be a big problem for them.”
Vaughan has questioned England’s mentality and their ability to keep in games for long periods.
“It’s their mentality I worry about. I want England to find it within and find that desperation from within.
“Whether that means they have to bring different personnel in is for them to decide, but they have somehow got to find that inner drive and belief of winning the key moments.
“Australia recognise the key moments and generally win them.
“I do now worry for them (England) in Perth, Melbourne and Sydney because the ball will not swing around as we have seen here.
“Over the two Tests, there has been nine and a half days and England have won one of them. You aren’t going to win many Test matches playing like that.”
Former batsman Geoffrey Boycott is not in any doubt where the problem lies.
“You have to bat better, you have to put runs on the board to give your bowlers chance,” he said.
“I know everybody says that bowlers win matches because they have to take 20 wickets but if you don’t make enough runs you’re always up against it and we just don’t make enough runs.
“I accept the Australian bowlers are better than England’s so it’s tougher but you knew that before you came and if didn’t you’re an idiot.
“When the chips are down, when the big moments came in Brisbane – there were two – the Aussies were better than us, the big moments come here, they are up for it and they are better than us.
“We have had half a day in 10 and that’s not enough. That’s why we are two down and the Ashes are nearly gone.”
Boycott described spinner Moeen Ali, who has taken just two wickets compared to Nathan Lyon’s 11, as England’s “weak link” and Graeme Swann says there should be a question mark over his place.
“He doesn’t deserve his place as a bowler and it will be a big call to bring in Mason Crane,” Swann said. “He (Moeen) has to score with the bat, he has to contribute and he has not done with either (batting or bowling) in this game.”
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England went 2-0 down in the series after falling to a 120-run defeat in the second Test in Adelaide as Australia took six wickets in the first session of day five.
England had resumed on 176 for four with hopes of a chasing down their victory target of 354 after fighting back on days three and four.
But they were soon ripped away as captain Root and Chris Woakes were dismissed without adding to their overnight total.
“Last night and leading into that we showed what we can do and we showed the side that we actually are,” Root told BT Sport. “We need to make sure we repeat those performances for longer periods of time.
“We came to the ground this morning well in the fight but unfortunately those two early wickets really did cost us.
“If we got in and went on and make a decent partnership there it is a completely different game. But, unfortunately, we just weren’t able to do that.
“It’s very frustrating, I thought the way we responded in the second innings with the ball and then the fight and resolve we showed last night with the bat was outstanding.
“It would have been nice to be two or three down going into today, but, credit where credit’s due, they bowled very well up front and we just have to be better.”
Root won the toss and opted to bowl, but his bowlers wasted helpful conditions as Australia were allowed to post a commanding first-innings total.
Given the chance again, though, Root insisted he would still make the same call.
“There are lots of things that you look back on and maybe do differently but that wasn’t one of them.
“I don’t actually (regret it), you want to give your bowlers the best chance to take 10 wickets and in those conditions with the quality that we have I fully expected those guys to take 10 wickets.
“With the rain around and losing some time potentially hampered us, we would have had 10 overs with the second new ball that night that were taken away from us under lights.”