Gordon Brown defended Ken Livingstone's record as Conservatives called for an inquiry into corruption allegations at the London Development Agency (LDA).
The Tories want an investigation into the LDA and the mayor
Metropolitan Police are investigating four projects at the LDA, which is the London Mayor's business arm.
Tory MP Greg Hands wants a Commons inquiry into the allegations, and into Mr Livingstone's role as mayor.
Gordon Brown said it was police matter and credited Mr Livingstone with reducing crime and improving transport.
The row centres on allegations that LDA contracts and funding were awarded to organisations because of their personal links with Lee Jasper, the mayor's senior aide and director of equalities.
The LDA conducted an internal review into "suspect" projects which concluded the claims of impropriety were unfounded.
But it has referred some allegations to the police because they have greater powers to investigate.
At Prime Minister's Questions, Mr Hands, MP for Hammersmith and Fulham, asked: "Will you join me and colleagues from across the House in calling for an independent investigation into corruption at the LDA and the role of Mayor Ken Livingstone?"
The prime minister replied: "That is a matter for the police.
"But if we look at London: jobs are up in London, police numbers are up in London, crime is down in London, transport is getting more investment. That's why we need a Labour Mayor."
Mr Livingstone came under pressure this week after a highly critical Channel 4 Despatches documentary - dismissed by his team as a "hatchet job" - and the departure of Mr Jasper's deputy, Rosemary Emodi.
Last week she denied visiting a £200-a-night resort in Nigeria last November.
But when the BBC London confronted her on Tuesday with evidence she flew there Ms Emodi immediately tendered her resignation.