State Home Minister Ramesh Chennithala said the decision to initiate further probe was taken after the Crime Branch examined the revelations made recently on the Swami's death and was convinced that the case qualified for further investigation.
A report was submitted to this government in this regard, he told a press conference at Alappuzha.
"Government is convinced that there are new revelations on the issue," he said.
Triggering a controversy last month, Kerala Bar Hotel Owners Association Working President Biju Ramesh, also leader of Sree Narayana Dharam Vedi, rival to SNDP, had alleged that the Swami was murdered and that Natesan and his son Thushar had a role in it.
The ordering of further probe just ahead of November 2 civic polls assumes political significance as it comes in the wake of BJP striving to get the support of the SNDP, an organisation of backward Ezhava community headed by Natesan, to form a third Front in the state.
Chennithala said further probe has been ordered under CrPc 173(3) in view of the fresh revelations on the death of the Swami, former head of Sivagiri Mutt, who was found drowned in the Periyar river at Aluva in July 2002.
Following the new revelations in the case, members of the Swami's family, who had expressed suspicion over the death, recently submitted a petition to government for further probe.
The issue had evoked heated debate in the state with demand for a fresh probe coming from different quarters including from Swami Prakashananda, the present head of Varkala-based Sivagiri mutt, founded by eminent social reformer Sree Narayana Guru.
As per the government decision, Crime Branch ADGP Ananthakrishnan would supervise the probe to be carried out by a special team headed by Ernakulam Superintendent P K Madhu.
Natesan, who had rejected the allegations and recently announced decision to form a new political party in the state, welcomed the government decision for further probe.
"Let the truth come out and clear all doubts. Nothing is going to happen to me," he said, adding, "the decision of further investigation is actually a cruelty to the Swami who attained 'jalasamadhi'."
Ramesh had alleged that Swami was murdered by one Priyan, a convict in a murder case now in prison, on behalf of Natesan. He had also alleged that Natesan's involvement in the murder was conveyed to him by Priyan himself.
Both Natesan and Priyan have rejected the allegations. Natesan had earlier said he was ready to face any probe, including by the CBI.
An earlier investigation by Crime Branch had concluded that Swami's death was a case of drowning and had submitted a report for the closure of the case in 2012. Meanwhile, CPI-M State Secretary Kodiyeri Balakrishnan said the government's decision to announce further investigation was an attempt to divert the attention from the special vigilance court verdict ordering further probe against state Finance Minster K M Mani in the bar bribery case.
"Anyway, the party welcomes the decision for a further investigation in Swami's death. But, it should have been announced earlier," Balakrishnan said.