Union home minister Rajnath Singh, whom the Intelligence Bureau reports to, had earlier said that efforts were on to secure the trooper's release from Pakistani captivity. Asked whether the soldier was a deserter, he did not reply.
A formation of the army had been the first to call Chandu Babulal Chavan, 22, of 37 Rashtriya Rifles a deserter but army headquarters had said he had strayed inadvertently across the border from Poonch in Jammu.
(Indian and Pakistani sources have referred to the jawan as "Chohan" but his relatives in Maharashtra said the name was "Chavan". The Rashtriya Rifles is a counter-insurgency force.)
"Attempts are being made to secure the release of the Indian soldier who is in Pakistan's custody," Rajnath told reporters at North Block this morning after chairing a high-level security review meeting.
In the evening, an Intelligence Bureau source said: "Our findings have revealed that he was not part of the army's Special Forces teams that carried out the surgical strikes early on Thursday morning. He crossed over on his own a few hours after the surgical strikes."
The source said the trooper had "crossed over with arms and ammunition".
"He is a deserter. Only a thorough probe will reveal why he went across," the source said.
"We need to question him to get to the bottom of the story but Pakistan won't release him anytime soon amid the heightened hostilities following the surgical strikes."
Government sources said the foreign ministry would be asked to try and secure Chavan's release by working the diplomatic channels after the tensions ease.
Pakistan had initially claimed to have captured the jawan from his post in Mendhar sub-sector yesterday afternoon but India's army denied it.
Later, army headquarters in India said he had strayed across and that the two directors-general of military operations had spoken over their hotline to secure his return. Subsequently, the Pakistani army denied that an Indian soldier had been captured.
"There's a lot of confusion," a home ministry official acknowledged.
Intelligence Bureau director Dineshwar Sharma and Research & Analysis Wing chief Rajinder Khanna attended the hour-long security review at North Block, as did national security adviser Ajit Doval and home secretary Rajiv Mehrishi.
The BSF has been asked to step up vigil along the 2,500km international border with Pakistan that stretches from Jammu and Punjab to Rajasthan and Gujarat.
Sources said Rajnath met the CISF director-general and asked him to intensify security at all the country's airports.