Police spokesman Ruwan Gunasekara said former Defense Secretary Hemasiri Fernando and police chief Pujith Jayasundara were arrested at hospitals where they had been admitted. They remain in the hospitals under police custody, he said.
The arrests came a day after prosecutors asked police to explain why they had not arrested the two former senior officials despite being instructed to do so.
The attorney general's department said in a letter to acting police chief C.D. Wickremaratne on Monday that it had ordered Fernando and Jayasundara to be named as suspects and produced before a court because a presidential commission of inquiry found grounds to charge them with dereliction of duties and criminal negligence.
The letter said crimes the officials are suspected of having committed fall within "grave crimes against humanity" under international law.
Police had reportedly sought to question Fernando and Jayasundara but did not because they had been admitted to hospitals.
Fernando resigned after the blasts and Jayasundara was sent on compulsory leave.
Since the April 21 suicide attacks, the government has acknowledged it received intelligence reports about the plot beforehand but failed to act on them.
Both Fernando and Jayasundara appeared before a parliamentary committee inquiring into the blasts and described the security failures. President Maithripala Sirisena, however, opposed the parliamentary committee conducting a separate inquiry while court cases were being heard on the blasts.
Fernando told the committee that Sirisena wasn't easily accessible for discussions. Jayasundara said Sirisena asked him after the blasts to resign to take responsibility and promised he would have his name cleared in any subsequent inquiry.
Jayasundara also said Sirisena had asked him not to attend National Security Council meetings since last October, when Sirisena fired Prime Minister Ranil Wickremesinghe in a power struggle that triggered a seven-week political crisis. Wickremesinghe was subsequently reinstated by the Supreme Court.