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The striker, whose attempts to join Chelsea are being blocked by United, played no part in United's tour of the Far East and Australia last month because of a hamstring injury.
And United said that a right shoulder problem kept Rooney out of the trip to Sweden earlier this week after he played in a behind-closed-doors training match against Real Betis last weekend.
But with key World Cup qualifiers looming next month, coach Roy Hodgson is confident Rooney will have recovered to face Scotland on Wednesday at Wembley Stadium as the rivals meet to mark the 150th anniversary of the English Football Association.
"Obviously he is very short of match practice but the important thing is that he is physically fit to play and then it will be up to us to decide how many minutes he can play because it is a bit naive to think he can play for 90 minutes," Hodgson said.
Rooney trained with United's reserve team on Thursday. While United insists that he is not for sale, the 27-year-old forward is unhappy that he fell down the pecking order at Old Trafford last season.
"In an ideal world, you want your key players playing first-team football but we will have to see what transpires there," Hodgson said.
"There is always going to be that situation.
"I'm sure it won't be the first time this season when I am asked why I have selected a player who is not good enough to play for his club side."
While Rooney is looking to make his 84th England appearance at Wembley Stadium on Wednesday against Scotland, Southampton striker Rickie Lambert was called up for the first time at 31 hours after his partner gave birth to a girl.
"What really impressed me about him is that this is a man who has come up the hard way starting in non-League," Hodgson said.
After moving from Bristol Rovers to Southampton in 2009, Lambert helped the south-coast club gaining promotion to the Premier League in 2012.
Now he'll be competing for a spot up front alongside Rooney, Jermain Defoe and Danny Welbeck.
"He is a man who has worked hard to prove himself over all these years and deserves his call-up at a time when a couple of players like Daniel Sturridge and Andy Carroll, who might have got the nod ahead of him, are unavailable," Hodgson said, before stressing: "We are short of forward players. If you go through all of the candidates, you still don't get to more than seven or eight."
The priority for Hodgson is taking England to Brazil next June.
England is second in its World Cup qualifying group, two points behind Montenegro with five games remaining. In September England hosts Moldova before traveling to Ukraine.
"I am confident that the team will not let the country or themselves down," Hodgson said.
England squad to face Scotland:
Goalkeepers: Ben Foster (West Bromwich Albion), Joe Hart (Manchester City), John Ruddy (Norwich).
Defenders: Leighton Baines (Everton), Gary Cahill (Chelsea), Ashley Cole (Chelsea), Phil Jagielka (Everton), Glen Johnson (Liverpool), Phil Jones (Manchester United), Chris Smalling (Manchester United), Kyle Walker (Tottenham).
Midfielders: Michael Carrick (Manchester United), Tom Cleverley (Manchester United), Steven Gerrard (Liverpool), Frank Lampard (Chelsea), Jack Wilshere (Arsenal), James Milner (Manchester City), Alex Oxlade-Chamberlain (Arsenal), Theo Walcott (Arsenal), Ashley Young (Manchester United), Wilfried Zaha (Manchester United).
Forwards: Jermain Defoe (Tottenham), Rickie Lambert (Southampton), Wayne Rooney (Manchester United), Danny Welbeck (Manchester United).
