Police had reportedly sought to question Fernando and Jayasundara but did not because they had been admitted to hospitals.
Attorney General Dappula de Livera wrote to the acting police chief urging him to bring charges against his predecessor Pujith Jayasundara and the former secretary to the Ministry of Defence, Hemasiri Fernando.
"There is sufficient information to prove negligence of official duties ... and criminal negligence". For lesser charges of negligence leading to damage of property, they could face up to 52 years in prison.
"This incident that took place was due to gross negligence on their part and constitute crimes that fall into the category of "grave crimes against humanity" under global criminal law", the AG said in letter.
Based on the report issued by the Special Board of Inquiry, the Attorney General had earlier directed the Acting IGP to initiate criminal investigations against nine high ranking police officers.
Jayasundara and Fernando were not immediately reachable for comment, though both had previously appeared before a parliamentary committee investigating the attacks and denied the allegations.
It comes after advance warnings from intelligence services in India that attacks were being planned were ignored.
The two men had previously accused President Maithripala Sirisena of negligence in his assessment of possible national security threats.
Some 45 foreign nationals were among the dead and 500 people were injured in the attacks.
The government, after the Easter attacks, has acknowledged it received intelligence reports about the plot beforehand.
The president has objected to a parliamentary investigation into the attacks and ordered police not to co-operate.