The gold reliquary was stolen at the weekend from a small stone church, San Pietro della Ienca, in the mountains east of Rome, where, in his younger days, the pope would slip away secretly from the pressures of the Vatican to hike and ski.
"I appeal to those who carried out this deplorable act," Archbishop Giuseppe Petrocchi of the city of L'Aquila said in a letter to local Catholics on Monday night.
"Give it back," he said.
Many Catholic churches have reliquaries, usually small, ornate containers that hold relics, in some cases body parts of revered church figures.
The one stolen at the weekend contained a blood-soaked piece of cloth, most likely from the cassock John Paul was wearing on May 13, 1981 when he was shot in an assassination attempt, the office of Monsignor Slowomir Oder, the official in charge of John Paul's sainthood cause, told Reuters.
Oder's office could not specify how many such blood relics of John Paul existed but said Italian media reports that there were only three in the world were wrong.
Dozens of police with sniffer dogs were still scouring the remote, snow-blanketed area for clues on Tuesday.
Franca Corrieri, a custodian of the church, told Reuters she had discovered the break-in on Sunday morning when she saw that window bars had been sawn off.
Police found only the gold reliquary and a crucifix missing even though the thieves would have had time to take other objects during the night-time raid in the isolated area.
This led them to believe the theft might have been commissioned or that the thieves may intend to seek a ransom.
John Paul is due to be made a saint of the Roman Catholic Church in May, meaning the relic will become more valuable.
The pope, who died in 2005 after reigning for 27 years, loved the mountains in the Abruzzo region because they reminded him of those in his native Poland.
In 2011, John Paul's former private secretary, Cardinal Stanislaw Dziwisz, now archbishop of Krakow in Poland, gave the local community the relic as a token of the love he had felt for the area.