Police spokesman Ruwan Gunasekara told Xinhua news agency that Fernando and Jayasundara were taken into police custody while they were both receiving treatment in two separate hospitals in capital Colombo.
Gunasekara said the Criminal Investigations Department (CID) would record statements from them but the two officials would continue to seek treatment in hospital.
Fernando was admitted to the Colombo General Hospital on Tuesday after which Jayasundara was also admitted to the Police Hospital over medical ailments.
Both were to appear before the CID on Tuesday to give statements over their alleged negligence in failing to act on information of possible terror attacks.
Attorney General Dappula De Livera, in a letter written to Acting Police Chief Chandana Wickremaratne on Monday, said that Jayasundara and Fernando could face charges of "grave crimes against humanity" for their alleged negligence in failing to prevent the attacks.
Following the attacks, Sri Lankan President Maithripala Sirisena blamed Fernando and Jayasundara for failing in their duties to act on an intelligence report which gave information of possible attacks on April 21.
Fernando was removed from his post by Sirisena following the bombings and Jayasundara was sent on compulsory leave. They deny all allegations against them.
The Islamic State had claimed the attacks which targeted three churches, three luxury hotels and two other locations.
( With inputs from IANS )