Dutch police arrested two people after a violent 14-hour stand-off at a house in The Hague, in which four officers were wounded by a hand grenade.
Police would not say if the arrests are linked to Van Gogh's murder
The two are suspected of "terrorist conspiracy with the aim of murder".
Anti-bomb experts were searching the apartment at the centre of the siege on Wednesday night for explosives.
Police said four people were detained in Amsterdam and one in Amersfoort as part of the same investigation into a network of radical Muslims.
Tensions have been high since filmmaker Theo van Gogh, who made a film critical of Islam, was shot dead in the street in a week ago.
A Muslim school in Uden was burned down earlier on Wednesday, and attacks have targeted Christian and Muslim buildings across the Netherlands.
The area where The Hague raid took place - near the Holland Spoor train station - was sealed off and airspace immediately over it was closed.
The building was surrounded by police in riot gear, fire engines, ambulances and special forces.
Police evacuated neighbours and they were bussed to local shelters.
"Around 1630 (1530 GMT), after special units fired teargas
into the apartment, two men were arrested," The Hague prosecutor Han Moraal told a press conference.
Police chief Gerard Bouwman said there had been an exchange of gunfire, and a hand grenade was thrown at the arresting officers, which exploded injuring several.
Two of the injured officers were reported to be in a serious condition.
One of the suspects was shot in the shoulder after he failed to obey police instructions, officials said.
The area remained sealed off on Wednesday night as police searched the apartment for explosives, the BBC's Geraldine Coughlan in The Hague said.
Warning to EU
Police would not comment on whether the arrests were linked to the murder of the filmmaker in Amsterdam a week ago.
Mr van Gogh had received death threats after the release of his latest film controversially portraying domestic violence in Muslim societies. It showed images of a semi-naked woman with Koranic script daubed on her body.
Six suspects, believed to be members of an Islamic militant group, remain in custody, including the alleged killer, 26-year-old Mohammed Bouyeri, who holds dual Dutch and Moroccan nationality.
"Theo, rest in peace" was scrawled on the Uden school walls
Dutch Prime Minister Jan Peter Balkenende told parliament that extremism was undermining democracy.
"It is the joint task of Muslims and non-Muslims to warn young people against radicalisation," he said, according to the Associated Press news agency.
The Dutch Immigration Minister, Rita Verdonk, has warned that EU countries are at risk, because of an increasing radicalism among young Muslims.
She said member states must act urgently to improve the integration of foreigners.
The minister, whose nation holds the EU presidency, said countries must ensure that immigrants learn the local language and accept Western values, but she said the EU also needed to develop, in her words, a common vision of integration.
Last week EU leaders agreed to create a common asylum system by 2010 to try to prevent illegal immigration into the EU.