"He was turned over to us by the MILF," said Major-General Ben Dolorfino, referring to the Muslim separatist guerrilla group the Moro Islamic Liberation Front (MILF).
The MILF maintained Thursday that it was not behind the kidnapping, as earlier alleged by the Philippine government, and that it was responsible for securing his release.
"We got Father Sinnott," Mohaqer Iqbal, the MILF's chief negotiator for the MILF in peace talks with the government, told AFP.
Dolorfino said Sinnott recounted to him that MILF emissaries went up to the kidnappers' jungle hideout last week and obtained his custody from the gunmen.
Rafael Seguis, the chief government negotiator in planned peace talks with the MILF, also told reporters that Sinnott was released voluntarily by the kidnappers.
Seguis and Iqbal had been meeting in recent months to try to restart peace talks, which were suspended last year after the MILF launched a series of deadly raids on Christian settler communities in Mindanao.
The 12,000-strong MILF has been waging a rebellion for an independent Islamic state in the southern third of the mainly Catholic Philippines since 1978.