A painting that was feared to be a later, inferior copy of a Botticelli masterpiece has been revealed as a rare original produced by the artist’s own workshop, English Heritage has revealed.

The artwork, a study of the Madonna and child entitled the Madonna of the Pomegranate, had been covered in thick layers of yellow varnish and substantial areas of overpainting, obscuring the fine brushwork underneath and leading to fears it was a poor-quality imitation.

But after its first restoration in more than a century, experts have confirmed the circular painting was made in the workshop of Sandro Botticelli in Renaissance Florence – though they are tantalisingly unable to be certain whether the master himself worked on it.

Bought by the diamond magnate and art collector Julius Wernher in 1897, the painting hung in a number of grand English homes until Wernher’s collection was loaned to English Heritage several decades ago, and put on display at Ranger’s House in Greenwich, south London. A larger version of the same painting by Botticelli hangs in the Uffizi gallery in Florence.

Restoring the artwork has taken several years, said Rachel Turnbull, English Heritage’s senior collections conservator, allowing a number of scientific tests which, along with expert examination of the newly revealed brushwork, confirmed the painting’s original provenance.

“Botticelli is very recognisable, and if you know even a little bit about art history, you would look at this painting and say, that’s a Botticelli. But, for sure, there are things out there that purport to be a Botticelli and probably aren’t. So we just wanted to be very careful about what we were saying.”

Infrared examination, X-ray testing and pigment analysis all pointed to the correct date, but, she said, it was when the overpainted halo on the Christ child was painstakingly removed that she knew the painting was correct.

“We thought long and hard about whether we would take off that later halo. When we eventually decided to do it, we found the evidence underneath of the original halo, but it was slightly in a raking light. I ducked down to pick something up, and I looked up and I could see this perfect pattern of the original halo and I thought, ‘Bingo, we’ve got it.’ It absolutely looks like other things of that from his workshop.”

It is possible that Botticelli could have worked on parts of the painting, she said, but the team have been unable to prove it. “Of course we would have loved to be able to say it’s the hand of the master. But that’s missing the point a little bit. If you were a 15th-century man who wanted to buy a painting like this, you bought a Botticelli, not a Botticelli workshop piece – that’s what you thought you were getting.”