Flood missed Leicester's Aviva Premiership victory over Saracens on Saturday with an ankle injury that could keep him out of the final against Harlequins on May 26.
England leave for South Africa on May 31 for a five-match tour that includes a three-Test series against the Springboks, with the first game on June 9.
"Clearly there is no point taking someone who is not available until halfway through the tour," Lancaster said.
"If there is a chance of him being fit in the few days after (the Premiership final) then perhaps we would (take him).
"He has an ankle injury that will take a couple of weeks. It will depend very much on what our physios and the Leicester physios think at the time.
"Hopefully he'll be right for the final and the tour. I have to make sure I have enough cover for South Africa."
If Flood is ruled out, Gloucester fly-half Freddie Burns is the next in line having today been added to the England squad for the non-cap international against the Barbarians on May 27.
Lancaster, who is without his Leicester and Harlequins contingent, has also drafted in scrum-halves Haydn Thomas and Richard Wigglesworth plus London Irish flanker Jamie Gibson.
Dylan Hartley will also be involved in his first match back since he was banned for eight weeks for biting Ireland flanker Stephen Ferris.
Hartley has been described as a future England captain by forwards coach Graham Rowntree although Phil Dowson appears the likely leader of the 27-man squad.
"We have a leadership group in mind - Phil Dowson, Ben Foden, Brad Barritt, Charlie Hodgson, Dylan, those sorts of guys," Lancaster said.
Chris Ashton will also play if he has recovered from a back injury but Alex Corbisiero (biceps) and Ben Morgan (hamstring) are not expected to be ready in time.
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