Social workers removed Col. Hilton Corder's two young daughters from the home where he lives with his wife, TV weather forecaster Deborah Martorell, said Col. Fausto Morales, who is investigating the allegations.
The children were later handed over to Martorell, who is staying with them at a different place, Morales said. He said police have removed all weapons from Cordero's house and are interviewing the couple and the children.
Corder requested Friday that he be temporarily relieved of his duties because "he is facing a delicate family situation that required his full attention," San Juan Mayor Jorge Santini said in a statement.
"We have nothing to indicate that there are problems in their marriage," Morales said. He did not comment on the allegations of molestation.
Morales declined to give the children's exact ages, except to say they range from 4 to 14 years old.
Cordero's private home number is not listed, and he could not be reached for comment. It is unclear if he has an attorney.