Speaking at a news conference in Newcastle, Allardyce said the striker had suffered a torn thigh muscle and also had a suspected weakness in his stomach area which may require surgery.
"He will be back for the first game after the England internationals at the very, very earliest," Allardyce was quoted as saying on Newcastle's Web site (www.nufc.co.uk).
"If he does have surgery we will be managing two situations and one might clear up quicker than the other."
England have Euro 2008 qualifiers in Group E against Estonia on October 13 and Russia four days later. The first match Owen might be able to play would be the home Premier League game with Tottenham Hotspur on October 22.
Allardyce said there was no chance of Owen being rushed back into playing before he was totally fit.
"The full picture is that he has not got a hernia but there may be a weakness in the stomach area which may have contributed to the adductor muscle tear.
"So while he is out for two or three weeks with that tear we are sending him to a specialist in Germany who will assess him and if there is any surgery needed to strengthen the area -- not repair a hernia -- that will be undertaken there.
"That should clear up both problems and allow Michael Owen to hopefully push on to play more and more games on a regular basis.
"For him and for us it's disappointing but we have to manage and get on with it."
Owen has been plagued by injuries since December 31 2005 when he broke a metatarsal playing for Newcastle at Spurs which kept him out almost until the end of the season.
He then injured his knee playing for England at the World Cup finals, and missed all but the last three games of last season.
In July he injured a thigh in pre-season training and missed the first game of the season, but had scored five goals for England and Newcastle before tearing his groin.
He limped out of Newcastle's 1-0 defeat at Derby County last week and also failed to finish Newcastle's 3-1 win over West Ham United on Sunday.
England coach Steve McClaren is already without Emile Heskey, Owen's strike partner in the games against Israel and Russia, for the vital matches in October.
Heskey broke a metatarsal playing for Wigan against Fulham on September 15.
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