The committee, dominated by Aquino allies, voted 54-4 against each of the complaints, declaring them insufficient in substance.
The complaints were filed by mostly left-wing activists and sponsored by the House's left-wing bloc.
They charged Aquino of culpable violation of the constitution, betrayal of public trust and corruption.
The complaints cited Aquino's implementation of a major economic stimulus program declared partly unconstitutional by the Supreme Court and a defence cooperation agreement that gives American troops greater access to bases across the Philippines. Aquino has denied any wrongdoing.
"Mr. Chair, this is really a terrible day for accountability, a terrible day for the congressional power over the purse, a terrible day for the Filipino people," said Rep. Neri Colmenares, one of the sponsors of the complaints, addressing Rep. Neil Tupas, the committee chairman.
About a dozen youths who raised protest banners and chanted "Oust Noynoy!" had to be forcibly evicted from the room by security personnel. Noynoy is Aquino's nickname.