By a vote of eight to seven, the 15-member court dismissed the "People's Initiative" petition to change the Philippine system of government.
The court ruled the petition to hold a referendum on switching to a parliamentary form of rule would be illegal because only Congress can pass such sweeping revisions to the constitution.
Court Spokeswoman Gleo Guerre explained the decision in Manila.
"Under the constitution, the People's Initiative can only apply for amendments to the constitution," she said. " And the proposed changes to the constitution, according to the court, constitutes revisions."
President Gloria Arroyo's government had backed the petition for a public vote on adopting a parliament. Her allies had secured more than six million signatures to endorse it.
But Guerre says the Supreme Court - in throwing out the petition - also questioned the legitimacy of those signatures, saying it was not clear if people knew what they were signing.
"The court found that the signatures were obtained irregularly, because they were just placed on the signature sheet and they were not appended [attached] to the actual petition containing the text of the proposed changes. In short, there was a lack of adequate showing that the people who signed knew the changes that they are affixing their signatures to," she said.
Advocates, including the president, had been pushing to switch to a parliament from the current American-style two-chamber Congress as a means to end political deadlock between the opposition controlled Senate and the administration-friendly House of Representatives. President Arroyo has argued this would bring faster policy making and greater economic growth.
Opponents of the charter change, known here as "cha cha", say Mrs. Arroyo, who has survived two impeachment bids and at least one coup attempt, was just trying to eliminate her opponents in the Senate. They note it could have allowed her to stay in office after her term ends in 2010.
Senator Franklin Drilon, a key opponent of the Mrs. Arroyo, hailed Wednesday's decision, saying it shows the independence of the court in the face of what he called 'brazen pressure.'