Lt Col Muhammad Habib Zahir disappeared on April 6 from Lumbini, a Buddhist pilgrimage site near India's border town of Sonauli, where he had apparently gone for a job interview.
Foreign Office spokesperson Nafees Zakaria said Zahir was "trapped" and Pakistan was in touch with Nepal to trace him.
"He was lured after being offered a job... The role of foreign spy agencies cannot be ruled out," he said, without naming any country.
Zahir, who retired from service in October 2014 from the artillery wing of the Pakistan Army, worked for a private firm but had posted his profile online seeking another employment.
A caller, who identified himself as Mark Thompson, had reportedly contacted Zahir - via email and telephone - for the job interview and he was provided an air ticket to travel to Nepal.
An initial probe by Pakistani security agencies has showed that a phone number registered in the UK was computer- generated to contact Zahir and emails and website domains were registered in India.
His disappearance has coincided with the death penalty handed down to former India naval officer Kulbhushan Jadhav by a Pakistani army court for his involvement in "terrorism and espionage". But Pakistan has repeatedly refused India any consular access to Jadhav.
The sentencing has evoked strong reactions from India, with External Affairs Minister Sushma Swaraj saying the country will go out of its way to secure Jadhav's release.
Today, Zakaria warned against linking Zahir's case with Jadhav's as the Indian national was an "irrefutable proof of Indian state's involvement in terrorism, subversion and terror financing."
He said the "R&AW agent was arrested red-handed", who identified himself and has "confessed" in their custody.
The foreign office spokesperson also said four terrorists arrested by Sindh Rangers yesterday from Karachi have "confessed" to having "links" with the R&AW.
"India remains involved in subversive and terrorist activities and terror financing in Pakistan. Kulbhushan Jadhav is an irrefutable proof. The arrest of four terrorists by Sindh Rangers, yesterday, is also a case in point," he said.
"Prime Minister Narendra Modi during his visit to Bangladesh [also] confessed to India's involvement in [then] East Pakistan in 1971," Zakaria said.
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