The decision on Wednesday leaves Arroyo in power despite a months-long campaign to unseat her for alleged vote fraud.
Arroyo's opponents have one last slim chance of impeaching her if they can win enough support in the full House by Monday but admit they are not confident of doing so.
The House of Representatives justice committee ruled that the remaining complaint against Arroyo, alleging she betrayed public trust through rigging the May 2004 vote, was sufficient in form but lacking in "substance".
The committee earlier in the day threw out the two other impeachment complaints, including one sponsored by the political opposition that accused the president of corruption and human rights violations.
"The three complaints have in effect been dismissed," House of Representatives Speaker and Arroyo ally Jose de Venecia said on television.
"I hope and pray that we can now begin the process of reconciliation in the House and in our country."
Lack of confidence
The key votes were made minus the opposition, which had walked out of the proceedings on Tuesday. They said Arroyo had rigged the congressional hearings as well as last year's vote, turning the process into a farce.
The earlier two complaints were rejected because the constitution sets a limit of one impeachment complaint against an official within a year.
House opposition leader Francis Escudero said they would concentrate on trying to win the support of at least 79 - one third - of the 236 members of the House of Representatives.
Many Filipinos made clear their
dissatisfaction at the decision
This is the minimum number required to overturn the justice committee rulings and compel the House to ask the Senate (upper house) to try Arroyo.
"We're hopeful but not confident," Escudero said. "Even if we get 79, it won't be a walk in the park."
Short of support
Legislator Edmund Reyes earlier told the committee that the opposition impeachment complaint is now backed by the signatures of 50 House members, with 23 others committing their support in principle - leaving it just six short.
Escudero said his camp has until Monday to gather the 79 signatures. On the same day, de Venecia said the entire House membership will meet in full session to ratify the justice committee's actions.
De Venecia said that theoretically, the opposition could still muster the required 79 votes by Monday. If that happens, he said, "it will be my duty to send it to the Senate for trial".
The last outstanding complaint, filed by activist lawyer Oliver Lozano in June, accused Arroyo of betraying public trust by allegedly calling an independent election official before Congress could proclaim the winner of the presidential election.
However, the justice committee ruled that the evidence used to back the Lozano complaint was inadmissible because it relied on illegally wiretapped conversations allegedly between Arroyo and a senior election official.
The 58-year-old US-educated economist has been under fire since an audiotape was leaked in which a woman sounding like her apparently tells a senior poll official to fix the outcome of the polls.
Arroyo said she had erred in calling an electoral official before Congress could proclaim the winner. But she denied any wrongdoing, saying she was merely trying to protect her vote against any attempt by her opponents to cheat, and refused to resign.
Arroyo has denied doing
anything wrong in the elections
Her admission sparked mass cabinet resignations and defections from key allies who urged her to step down for the good of the nation.
But attempts to whip up People Power demonstrations in the streets, like those that brought down two of her predecessors, largely fizzled out.
As debates were raging on Wednesday, House security officials and riot police armed with truncheons and shields clashed with dozens of anti-government protesters outside Congress.