Thousands marched to condemn the murder
The suspect, a 32-year-old Dutchman identified as Volkert van der Graaf, appeared at a closed hearing before an Amsterdam judge. He refused to make a statement.
He was allegedly caught with a pistol moments after the fatal shooting of Fortuyn, which shocked the Netherlands.
The murder, outside a radio station in the central Dutch city of Hilversum on Monday, came just over a week before Fortuyn was due to contest the country's general election.
The public prosecutor said ammunition found at the suspect's house matched the calibre of the bullets which killed Fortuyn.
Police also removed environmental literature from the man's home in the town of Harderwijk, 50 kilometres east of Amsterdam.
Custody
The suspect, an activist with the group Environmental Offensive, will appear before three trial judges in 10 days' time. They will then decide if he can be held for another 30 days.
Under Dutch law a suspect can be detained for 100 days before being formally charged and brought to trial.
The suspect is also reported to be an animal rights activist. He is believed to have acted alone and did not have a gun licence.
Murder is punishable by up to 20 years in prison in the Netherlands.
Strong poll showing
The court appearance came as the Netherlands was still adjusting to the shock of the murder.
Thousands rallied in the city of Rotterdam, Fortuyn's home and power base, on Tuesday evening to protest about the killing.
Opinion polls had suggested that Fortuyn, 54, would win 15% to 20% of the vote in the 15 May election, with his policy of restricting immigration to the Netherlands gaining him substantial support.
His name will still appear top of his party's list of 52 candidates.
Sympathy vote
The BBC's Paul Anderson in Rotterdam says it seems likely that the party - which is called Fortuyn's List - will gain from the sympathy vote.
He says that if the opinion polls are borne out, the election could leave the party holding the balance of power in the Dutch political system.
The murder has caused consternation across Europe, with leaders expressing horror that such violence could erupt on the Dutch political scene.
The BBC's Tim Franks in Rotterdam says that many people who marched against the killing on Tuesaday night did so to express their sorrow that this should happen in the easy-going Netherlands, rather than to show political support for Fortuyn.
Multiple injuries
Fortuyn came to prominence in March when his party made a strong showing in local elections in Rotterdam.
He provoked public indignation by calling for the Netherlands' borders to be closed to immigrants, and by describing Islam as a "backward" religion.
He was shot six times, suffering multiple wounds in the head, chest and neck, and died shortly afterwards.
Fortuyn's funeral will be held on Friday, and his remains buried at a favourite spot in northern Italy where he had a holiday home.