On 27 August 2009, armed men abducted him and freed him on the following day.

Ekneligoda had told his friends that he had been taken to the Panagoda Army camp, where his handwriting had been checked.

The CID too, questioned his friend Kelly Senanayake regarding the journalist’s handwriting.

Several websites have reported that that had been done to compare Ekneligoda’s handwriting with handwriting in the script of ‘Pavul Gasa’, a book written against the Rajapaksas.

However, Ruwan Ferdinandis, who was in charge of the book’s publisher SLFP Mahajana faction’s propaganda activities, said Ekneligoda had nothing to do with the book or any other activity pertaining to the book.

However, the missing journalist had written an article titled ‘Raja Pavulai Maavavuloi Elleegana Ratama Hapai’ and excerpts of the article had been included in the ‘Hansa Sandeshaya’ election propaganda newspaper a few days before his second abduction.

Meanwhile, a website being run overseas says abductors had compared handwriting in envelopes containing human ashes received by Temple Trees and the presidential secretariat with that of Ekneligoda.