The tribunal sternly warned Gutierrez it would cite her for contempt if she fails to do so.
If there is probable cause, Gutierrez should then file charges with the proper court and report to the SC on the progress of the case every three months, the SC said.
The court order stemmed from a petition filed by the Information Technology Foundation of the Philippines asking for action on the case.
Senate Minority Leader Aquilino Pimentel Jr., who has also been calling for action, said election officials involved should be held accountable and replaced in time for the 2007 mid-term elections.
In 2003, the Comelec purchased nearly 200 ballot counting machines from Mega Pacific at the cost of P1.2 billion.
However, in January 2004, the SC nullified the Comelecs purchase contract, citing irregularities in the contract awarding.
In a strongly-worded decision, the SC ordered the Ombudsman to investigate those involved in the Mega Pacific deal for possible criminal liability.
The court also ordered the Office of the Solicitor General to recover whatever money was paid to Mega Pacific for the machines.
The ruling, however, inadvertently derailed government plans to modernize the countrys antiquated electoral system, which is riddled with opportunities for poll fraud. It takes election officials weeks to complete the counting of votes.
President Arroyo is currently battling opposition allegations that she cheated her way to victory in the 2004 election.
She admitted having an inappropriate conversation with an election official before Congress declared the winner but denies manipulating the poll outcome.
Pimentel said Gutierrez should stop sitting on the case, pointing out that the Ombudsmans legal, monitoring and prosecuting division as early as October 2004 found prima facie evidence against those involved.
He said that Gutierrez could start by filing the necessary charges against four of the seven Comelec officials who signed the contract with Mega Pacific.
The four officials former commissioners Rufino Javier, Mehol Sadain, Ralph Lantion and Luzviminda Tancangco have already retired so Pimentel said that the Ombudsman should have no reason not to start filing cases against them.
The four former officials are no longer immune from criminal prosecution.
The three other officials still with the Comelec are Chairman Benjamin Abalos, Resurreccion Borra and Florentino Tuason Jr.
Pimentel was the first to file a complaint against the Comelec officials following the 2004 ruling of the Supreme Court that nullified the contract between the Comelec and Mega Pacific.
Pimentel said Gutierrezs predecessor Simeon Marcelo had promised to sign the resolution on the poll automation deal shortly before he resigned on Nov. 30, 2005.
He said that it is irresponsible for the Office of the Ombudsman as the "protector of the people" to ignore the findings of its legal, monitoring and prosecution division that the contract between the Comelec and Mega Pacific was grossly disadvantageous to the government.
Pimentel said that the issuance of a resolution by Gutierrez on the case would pave the way for the filing of graft charges against incumbent Comelec officials involved in the deal.
The resolution could also be used as basis for an impeachment complaint against Abalos, Tuason and Borra. Jose Rodel Clapano, Marvin Sy