The prosecutor will evaluate the evidence before forwarding the case to an anti-graft court, which will decide whether to issue arrest warrants.
The scandal caused such an uproar in the impoverished nation that hundreds of thousands of people turned up at a huge protest in Manila last month.
At the center of it is Napoles, who is accused of acting as a conduit for the money and a mastermind of the scam. She surrendered to President Benigno Aquino III in August after she was charged with illegal detention of a whistle-blower.
"This is a cleansing process," said Senate President Franklin Drilon.
One of the respondents, Sen. Jinggoy Estrada, who is a son of an ousted president, told his colleagues Monday that he was innocent. He said that Enrile, at 89 the oldest senator, was taken to a hospital over the weekend for high blood pressure but that he would challenge the charges in court.
The complaint has recommended the plunder charges be laid against Enrile, Estrada, Senator Ramon Revilla Jr. and two former members of the House of Representatives for allegedly pocketing more than 50 million pesos ($1.4 million) each.
Enrile said in a statement that the complaint was filed after an incomplete investigation.
"Let me make clear that I am innocent of the charges filed against me," he said.
Three other former House members are being accused of misuse of public funds, bribery and other corrupt practices for receiving less than 50 million pesos each. Napoles is named co-conspirator for both the plunder and the misuse of public funds charges.
A summary of the complaint said the scam starts with an agreement between a lawmaker and Napoles to designate her NGOs as recipients of special development funds that each member can allocate. The lawmaker allegedly then got 40 to 60 percent of the project's cash value as a kickback, while Napoles gave 10 percent to the head of the government agency implementing the project and pocketed the rest after deducting the cost of overpriced supplies.
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Associated Press writer Jim Gomez contributed to this report.