Saturday's game were grim, Fleming said there was concern about all aspects of the New Zealand game despite holding an unassailable 4-1 lead in the seven-match series.
"Part of the benefit of having a loss the other day was that we don't go thinking we are better than what we are," Fleming said.
"One thing we've been looking at in the last two days is rectifying our weaknesses in the coming games and when we first get to South Africa for the World Cup.
"We are under no illusions about what we're not doing well, but we still want to win games."
Fleming said that while he normally would not have batted first on the Wellington pitch, he chose to bat first because of a desire to see his team under more pressure after taking the series in Queenstown with a fourth straight win.
He got more than he bargained for as Zaheer Khan snared three wickets in nine balls to leave New Zealand reeling on 3-3, but still believed they had the chance to win.
His batsmen did not kick on to a score of 200, (they got 168) which India would have struggled to overtake.
"We want to finish off this series well," he said. "We should have won the game the other night but we did things that placed us under pressure and while we didn't cope that well, we still should have won.
"We now want to keep India guessing a little bit on the wickets and the way we're playing. We don't want to see them get something out of this series and go to the World Cup with a better feeling than us."
Fleming's India counterpart Saurav Ganguly said it was good to get the win, but said "we could have done better".
Ganguly, who was out first ball to extend his appalling run in New Zealand, said it was hard when runs were scarce.
"When you're captain of the side where most batsmen are struggling, you've just got to keep them going and tell them they have fantastic records in international cricket and it is a matter of one knock. I've got to tell myself that as well."
All of the Indian side were fit for the sixth match, Ganguly said, but Fleming must do without opening batsman Nathan Astle, who is out for the rest of the series with a recurrence of a patella tendon injury
One of the finds of the summer, Jaob Oram, also misses out after breaking a finger.
Mathew Sinclair will move up a place to partner Fleming as opener, a position where he scored back-to-back centuries in Sharjah last year.