Volkert van der Graaf is reported as saying he saw Mr Fortuyn's far-right views as a threat to vulnerable sections of society.
Mr Fortuyn was shot six times in the head, chest and neck outside a radio station on 6 May - just over a week before the Dutch general elections.
Mr Van der Graaf, 33, was arrested minutes after the shooting, carrying a loaded gun speckled with blood that matched Mr Fortuyn's DNA.
He is now likely to be formally charged with the murder in the next few weeks, after prosecutors finish their investigation and verify that, as he says, he was working alone.
Mr Van der Graaf "has admitted that he purposefully shot dead Fortuyn. He had conceived this plan some time earlier," the public prosecutor said in a statement.
"He saw in Fortuyn an increasing danger to, in particular, vulnerable sections of society.
"He was concerned about Fortuyn's prejudiced political views and the incendiary way [he] presented them and the substantial political power [he] seemed to be gaining."
Mr Fortuyn's brother, Marten, told the Dutch news agency ANP he was not surprised by the confession but felt irritated by Mr van der Graaf's presentation of himself as "the saviour of the nation".
Sympathy surge
The openly - and flamboyantly - gay Mr Fortuyn shattered the consensual, liberal image of Dutch politics with his anti-immigration views and assertion that Islam was "backward".
Mr Fortuyn's murder prompted a surge of sympathy and anger, and in the election that followed, his party Pim Fortuyn List (LPF) experienced a shock success, coming second in the vote.
But the three-way governing coalition that followed fell apart in under three months after LPF infighting.
Another election is scheduled for 22 January, though the latest polls suggest the LPF will retain fewer than a quarter of the 26 seats it currently holds in the 150-seat parliament.
However, the causes highlighted by Mr Fortuyn - concerning the integration of immigrants, crime and healthcare - continue to occupy centre stage in campaigning for the next election.