It is a storyline worthy of a Hercule Poirot whodunnit. After confiding in just 20 trusted people of his suspicion that a painting in his church was a lost masterpiece, a priest in the small Flemish town of Zele, 45 miles north of Brussels, has had to call in the local police over its sudden disappearance.

Pastor Jan Van Raemdonck, 61, turned to the detectives after two women laying flowers in the nave of the Sint-Ludgerus church last Friday morning discovered that the 16th-century painting, known as the Holy Family, had gone missing from its usual position by the altar.

The work, depicting Mary, Joseph and a sleeping baby Jesus, was due to be assessed within days by a respected Michelangelo expert, Maria Forcellino, after Van Raemdonck alerted her to its startling similarity to a drawing by the Renaissance master in the collection of the Duke of Portland.

Instead, Van Raemdonck, who has been a pastor at the church for five years, has been left to suffer an anxious wait. He estimates that the painting, donated to the church 16 years ago by a former Belgian senator, Etienne Cooreman, could be worth €100m (£89m), but the police are yet to offer any updates.

Facebook Twitter Pinterest The 16th-century painting, known as the Holy Family. Photograph: Jan Van Raemdonck

“A lady living nearby saw a young man, around 20 years old, near the church around 5am on Thursday morning, but he went away when she put her light on,” said Van Raemdonck. “On Friday morning at 9am, two ladies who were putting flowers on the altar noticed the external door was open and the painting was missing.

“I didn’t talk about my suspicion about the painting in the church,” he added. “I wanted to wait for the experts and if they said it was a Michelangelo I would have improved the security of the building. I only told some family, friends and the church’s council. I told about 20 people, and never in public.”

Van Raemdonck said he had emailed a number of museums as part of his research into the painting, but had not received a reply. “Maybe someone picked up the information from my emails,” he said. “I hope the police can check cameras in the area and find out what happened.”

The church believes it was a targeted burglary involving more than one thief. The painting, which is mounted in wood, is said to weigh about 100kg.

“They were only interested in that one painting,” Johan Anthuenis, the chair of the church council, told the Flemish newspaper Het Nieuwsblad. “They have not even looked at all other valuable items.”

Michelangelo was a prodigious producer of sculpture, sketches and paintings, and there have been a series of discoveries of lost works in recent years, albeit there are often years of tortuous attempts at verification.

In 2010, an unfinished painting of Jesus and Mary, knocked off a wall by a stray tennis ball 27 years previously, was found tucked behind a family sofa. It was subsequently valued at £190m by Antonio Forcellino, brother to Maria, the expert commissioned by pastor Van Raemdonck.

The mayor of Zele, Hans Knop, said a link between the theft and the pastor’s theory about the painting was plausible.

Van Raemdonck, an amateur writer of history and children’s books, who was working on a fictional novel about the painting before it disappeared, said: “It is a beautiful painting – I just hope we can get it back.”