Flood missed the Premiership semi-final victory over Saracens with an ankle problem and remains a doubt for the Tigers trophy clash with Harlequins a week on Saturday.
The 26-year-old also saw his preparations for the RBS 6 Nations hampered by injury and fell down the pecking order as Owen Farrell and Charlie Hodgson started in the No.10 jersey.
A fully fit Flood would challenge the Saracens duo but with England's first Test starting in Durban on June 9, Lancaster insists he won't be taking any risks.
"There's no point taking someone if he's not going to be available until halfway through the tour," said Lancaster. "It will depend on what the physios think."
Flood is not the only injury worry with winger Chris Ashton - known for his trademark swan dive celebration - missing Northampton's semi-final against Quins with a back injury.
"I don't know if he injured his back diving but there is a time and place for all these things," added Lancaster.
"As long as he gets it right with us that's all that matters to me. If I get the sense that people are doing things to promote themselves or that are selfish in nature I wouldn't be happy. But you wouldn't want to take the spontaneity and creativity out of Chris Ashton either."