Rooney sat out training when the 25-man squad met on Tuesday and he was absent from the latest session at St George’s Park on Wednesday morning.
The England captain suffered a knock to the ankle in Manchester United’s 3-0 defeat to Arsenal on Sunday.
It is understood that Rooney has been in touch with United manager Louis van Gaal on the matter.
Despite being a major doubt for Friday’s Euro 2016 qualifier against the Estonians, Rooney will remain with the England squad this week.
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It remains to be seen whether he will travel to Lithuania for the final qualifier of the campaign on Monday.
The 29-year-old is expected to attend Friday’s game at Wembley, even if he is not in the match-day squad, as he wants to pick up his commemorative golden boot for breaking Sir Bobby Charlton’s scoring record.
Rooney broke the 45-year long record with a penalty against Switzerland last month.
The 1966 World Cup winner will present Rooney with the boot before kick-off.
As part of the celebrations, a 20 metres squared surfer flag with Rooney’s picture on it will be passed over fans at Wembley on Friday.
The background of the surfer flag will be made up of tweets sent in by England fans.
The Football Association has also revealed a mural of the England captain will be unveiled in one of the concourses at Wembley before kick-off.
If Rooney misses the match, Hodgson has plenty of replacements available.
Harry Kane, Jamie Vardy and Theo Walcott could lead the line for the Three Lions.
Danny Ings is another striker in the squad, but he could miss out due to an ankle injury.
The former Burnley man, who is in the England squad for the first time, sat out training on Wednesday, as did Swansea midfielder Jonjo Shelvey.
Everton midfielder Tom Davies, who is with the England Under-17 squad, took part in training with the seniors on Wednesday after it became clear Shelvey would not be involved.
Andros Townsend and Kyle Walker were involved in the session. The Tottenham duo were drafted into the squad following the withdrawal of John Stones because of a knee problem on Tuesday.
England will make it nine straight qualifying wins if they overcome Estonia on Friday.
The FA is expecting a crowd of around 80,000-85,000 for the game innorth London.