The midfielder sat out Friday’s session because of illness and again did not take to the field 24 hours later. The European champions face Iran on Saransk on Monday.
Moutinho has been a key player for his country after starting both of their games so far in Russia and provided the assist for Cristiano Ronaldo in their 1-0 win against Morocco.
There was good news though as left-back Raphael Guerreiro returned to training after missing Friday’s session due to pain on his leg.
Portugal, who are level on four points with Spain, require just a point against Iran to qualify for the knockout stage.
The Tottenham midfielder suffered a minor thigh injury against Tunisia and has been rated as “unlikely” to feature in Nizhny Novgorod by England boss Gareth Southgate.
While Alli took to the field alongside his team-mates on Saturday morning, he participated in the warm-up before carrying out individual drills away from the main group.
England were completing their final preparations at the Spartak Zelenogorsk stadium before flying to Nizhny Novgorod.
Alli helped England clinch a 2-1 victory in their World Cup opener on Monday, when he looked set to come off in the first half after suffering a knock.
A scan confirmed a quad injury that needed to be managed this week.
Southgate told talkSPORT on Friday: “We have to wait and see whether Dele is going to be fit. It’s looking unlikely because he has not trained with the team yet, but he’s progressing really well, so we won’t rule that out just yet.”
Loftus-Cheek is seemingly poised to start England’s penultimate Group G game against Panama on Sunday as a replacement for Dele Alli, who is a fitness concern due to a minor thigh strain.
The 22-year-old has shown glimpses of star quality in his five international appearances to date and Hodgson is confident he will not be daunted on the world stage.
“I do think he’s ready, yes, definitely, 100 per cent,” the Crystal Palace boss told the Daily Mail.
Hodgson saw Loftus-Cheek at close quarters last season, with the highly-rated midfielder spending the entire campaign on loan at Palace.
And though he has been likened to former Chelsea and Germany great Ballack in the past, Hodgson thinks a more accurate comparison would be another England midfielder in Jack Wilshere.
“I’d say he goes by people more than Ballack did. I think he’s got Ballack’s power and his pace and his strength – he’s definitely got that,” Hodgson added.
“But he’s maybe got more strings to his bow than even Ballack had. That’s a bold thing to say, I know, but he’s so good at going past people. He’s got that deceptive turn of pace.
“In that way he’s a bit like Jack Wilshere really. That ability to receive a ball in tight situations and then come out very quickly on the other side and open a game up.
“That’s a skill because passing players can’t do that. Passing players have to pass it and then get it back again. Ruben can twist and turn his way out of tight situations and, as I say, open a game up. And then he’s very powerful going forward.
“I think he can add more goals to his game. I’m sure he will as time goes on.”