Four others were charged with forming an armed organisation and incitement to murder.
Samast, 17, who is reported to have been close to an ultranationalist group in his home town of Trabzon, has admitted to shooting Dink in daylight as he left the office of his newspaper, Agos, in Istanbul last Friday.
The murder brought 100,000 mourners to Istanbul's streets for Dink's funeral on Tuesday and has re-ignited debate about hardline nationalism in a country seeking European Union membership.
"From the quality and the nature of the crimes attributed to the suspects it is clear the result emerges that they formed an armed group," Engin told reporters late on Wednesday.
Engin said the fact that the suspects were remanded in custody did not mean that a case would be opened soon. Prosecutors will now prepare an indictment against the suspects.
Samast has confessed to killing Dink for "insulting" Turks in his writings and statements on the massacre of Armenians during World War One - a sensitive issue in Turkey.
Yasin Hayal, a well-known nationalist, has admitted to inciting his friend Samast to kill Dink, the police said.
Hayal served 11 months in jail for the bombing of a McDonald's restaurant in Trabzon in 2004.