The public prosecutor's office said it had asked parliament to lift the immunity of former Interior Minister Ljube Boskovski so he could be charged. A parliamentary committee was debating the request.
"It was a monstrous fabrication to get the attention of the international community. Only a sick mind can construct and give the order for such a gross liquidation of seven people whose destiny ended like in a horror movie," said Interior Ministry spokeswoman Mirjana Kontevska on Friday.
Boskovski has denied the allegations.
According to police sources, the prosecution said a police chief was told to find migrants who could fit the description of "Islamist terrorists".
They said the group, in fact economic migrants passing through Macedonia, was pin-pointed, kidnapped and killed in what security forces claimed was a coup against global terrorism.
"Nobody has the right on the basis of his own craziness to take someone's life in the name of the state," Kontevska said, in an apparent reference to Boskovski, who earned a reputation in office as an extreme nationalist.
She said the seven dead men, pictured in police photographs at the time with guns in their belts, were economic migrants passing through Macedonia on their way westwards.
Police sources said two of those in custody were generals in the police force and a further two men had been charged.