The Lankan Crime Investigations Department (CID) had summoned the four officers this morning to record their statements and they were subsequently taken into custody.
They include two lieutenant colonels, a sergeant and a Corporal, police spokesman Ruwan Gunasekera said.
"On the orders of the Inspector General of Police the CID began an investigation. This will be continued," Gunasekera said.
One of them was a rehabilitated member of the LTTE, Gunasekera said.
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Prageeth Eknaligoda disappeared in January 2010 just days prior to the presidential election held in the same month.
Eknaligoda, a cartoonist, had worked for the then opposition challenger - the former controversial Army chief Fonseka - who oversaw the military campaign against Tamil rebels in which thousands of civilians are said to have died.
Eknaligoda's disappearance became a major human rights thorn for Rajapaksa's regime which came under huge international pressure to probe the disappearance.
Maithripala Sirisena, who defeated Rajapaksa in presidential elections in January this year, had pledged fresh investigation into the case after quashing his previous convictions.
In March this year, the new government also conferred the highest military rank of field marshal on Fonseka after restoring all his political rights.