The student, identified as Onel de Guzman, 23, dropped out of college after his tutors rejected his software program, saying they did not condone theft.
Mr de Guzman lived in the apartment where the computer thought to be the source of the bug was kept.
The idea outlined in his thesis bears a striking similarity to the Love Bug virus which has caused havoc around the world since it appeared last week.
The BBC correspondent in Manila, John McLean, says there is a theory that Mr de Guzman could have unleashed the virus in revenge.
The bug, which spread via an e-mail bearing the line "ILOVEYOU", is believed to have affected at least 45 million computer users and caused billions of dollars of damage.
Suspicious
The Philippines National Bureau of Investigation (NBI) confirmed Mr de Guzman was one of several suspects wanted for questioning.
"His background is suspicious and his thesis was questionable because what he proposed was illegal," NBI deputy director Carlos Caabay said.
Mr de Guzman, a former student at the AMA Computer College in Manila, lived with Reonel Ramones who was arrested on Monday after a raid on their apartment.
He is said to be the brother of Reonel Ramones' girlfriend Irene de Guzman who lived in the same flat and is also wanted for questioning.
Investigators had pinpointed a computer at the apartment as the source of the bug. They seized a telephone, wiring and computer magazines, but no computer.
Stealing
In his thesis, Mr de Guzman said his software would "be helpful to a lot of people, especially internet users, to get Windows passwords" and spend more time on the internet without paying.
"We spend a lots of money to pay [for internet] accounts for only using a couple of hours," he wrote.
"So this program is the main solution. Use it to steal and retrieve internet accounts of the victim's computer."
But the thesis was rejected on 24 February. A college official noted: "This is illegal... We do not produce burglars."
AMA says Mr de Guzman dropped out after his paper was turned down.
Manuel Abad, executive vice president at AMA, said Mr de Guzman was a member of an underground computer group which provided programming to small businesses and wrote and sold thesis projects to computer students.
Codenames
FBI officials, who are helping the NBI, are said to have found 10 coded names embedded in the virus.
But the names could be pseudonyms of a single person or just a few people.
Experts say the Love Bug virus is likely to engender more variants in the coming weeks.
It affects only systems running Microsoft Windows with Windows Scripting Host enabled. Computers using Apple's operating system or Linux are not affected.