Abu Sayyaf militants, seeking independence for a province in the southern Philippines, also wanted to explode bombs in metropolitan Manila to try to get funding from the Islamic State, but the plans were uncovered, Aquino said, according to The Associated Press.
Aquino, whose six-year term ends in June, also said Abu Sayyaf may have been planning an assassination plot against him.
According to the AP, Abu Sayyaf is accused of beheading Canadian John Ridsdel on Monday in the Philippines after it did not receive the ransom it demanded. Pacquiao, perhaps the most famous Filipino in the world, was apparently also a kidnapping target for the group.
"They allegedly even hatched plots to kidnap Manny Pacquiao or one of his children, as well as my sister Kris or one of her children, with the plan to use them in bargaining for the release of their cohorts," Aquino said.
Pacquiao, who has five children, won world titles in a record eight weight classes from flyweight to junior middleweight. He announced his retirement following a unanimous decision victory against Timothy Bradley Jr. in their third welterweight fight on April 9 at the MGM Grand in Las Vegas.
Pacquiao, a two-term congressman in the Philippines, is running for one of 12 senate seats in the Philippines' national elections on May 9.
A spokesman for the fighter told ESPN he had not talked to Pacquiao about the alleged plot.