Officials declined to say whether the operation, which was continuing with suspects still in a building cordoned off by police in the Dutch seat of government at The Hague, was linked to the murder last week of a film-maker.
"On the request of criminal investigation branch, an arrest team this morning at 02:45 (0145 GMT) tried to arrest suspects in an ongoing probe by the crime squad into terrorism," chief justice official Han Moraal told a news conference at The Hague on Wednesday.
Moraal said three police officers were injured when a hand grenade was thrown at them. Shots were also fired, he said. An unspecified number of suspects were still in the building.
Two of the injured officers were in hospital while one had been allowed to go home, police said.
Officials said the airspace over The Hague had been closed amid the ongoing operation. They sealed off the area after the explosion and an anti-terrorism unit was on the scene.
"We are awaiting further police intervention," The Hague police spokesman Frans van Rijnswou said.
Fire engines and riot police were on the scene. Journalists were kept away from the building behind a cordon, and houses in the area were evacuated.
Dutch police have arrested 10
people in the Theo murder case
Dutch police have arrested 10 people in their investigation into the killing of film director Theo van Gogh last week and are still holding six, including the prime suspect Muhammad B, who has been charged with murder and suspected links to an armed group.
The Netherlands has seen a series of apparent tit-for-tat attacks since Van Gogh was murdered after being accused of insulting Islam with a recent film, including an arson attack on a Muslim school on Tuesday night, where the words "Theo R.I.P." were scrawled on the walls along with a "White Power" sign.
Van Gogh enraged Muslims with his film which said Islam promoted violence against women and showed Quranic verses written on a woman's semi-naked body. He was cremated on Tuesday evening.