The 26-year-old defendant has also been charged with membership of a group with "terrorist intentions".
"We will argue before the judge that he is at the centre of a criminal organisation and that the other arrested people are part of this group," prosecutor Leo de Wit told a news conference on Friday before the charges were formally laid.
The Dutch-Moroccan, identified by the nation's media as Muhammad B, was charged with the murder of film director Theo van Gogh, who was stabbed and shot as he cycled to work in Amsterdam on Tuesday, ANP quoted prosecutors as saying.
He was also charged with attempting to kill a policeman and a bystander, it added.
Police in Amsterdam say the
mood in the city is calm
The killing has revived memories of the murder of anti-immigration populist Pim Fortuyn by an animal rights activist in 2002 and stoked fears of heightened communal tension in a country where hostility towards Muslims and foreigners is on the rise.
The suspect, who De Wit said had maintained his right to silence, was also charged with conspiracy to murder prominent parliamentarian Ayaan Hirsi Ali and unnamed others.
A five-page letter pinned to Van Gogh's body with a knife was addressed to Hirsi Ali, a member of the VVD liberals.
"Dear Mrs Hirshi Ali (sic). Since you stepped into the political arena in the Netherlands you have been constantly busy terrorising Muslims and Islam with your remarks," the letter said, calling Hirsi Ali a "disbeliever fundamentalist".
Van Gogh's controversial film was written by the Somali born member of parliament Ayaan Hirsi Ali and claimed that Islam encouraged violence against women.
In the film Muslim women are portrayed wearing revealing variations of customary Islamic dress through which Quranic verses written on the actresses' half-naked bodies are clearly visible.
Dear Mrs Hirshi Ali (sic). Since you stepped into the political arena in the Netherlands you have been constantly busy terrorising Muslims and Islam with your remarks"
Letter pinned to Theo van Gogh's body
Police commissioner Bernard Welten said the mood was calm in Amsterdam but he had additional police out on the streets and had units on standby "to restore public order if needed".
In the central Dutch town of Utrecht, several fires broke out overnight at a new mosque belonging to a Moroccan religious association. A police spokeswoman said no evidence had been found of arson, but it was being investigated.
The Dutch cabinet said on Friday it was considering ways to combat violence, including stripping criminals with dual citizenship of their Dutch nationality, increasing police powers and boosting the budget of the AIVD security service.
Finance Minister Gerrit Zalm, who is also the deputy prime minister, told journalists the cabinet had also considered taking action against a mosque in Amsterdam, regularly attended by chief suspect, Muhammad B.
De Wit said six of the eight North Africans arrested in connection with the murder would also be charged for membership of a criminal organisation, while two others were freed.
NOS television news said two more suspects, both Moroccans, were released due to lack of evidence. One was illegally in the Netherlands and will be expelled.