The drawings will go on display at the museum under their new attribution in September - three years after being shown in an exhibition of Rubens' art at the National Gallery.
The painstaking detective work by Martin Royalton-Kisch is likely to cause controversy when the show opens later in the year. But Mr Royalton- Kisch, a curator in the museum's prints and drawing department, is convinced his theory will soon be accepted by the art world.
The clinching factor is a close analysis of handwriting on one of the drawings, of a dead tree covered in brambles at the Duke of Devonshire's Chatsworth estate.
Mr Royalton-Kisch claimed he became suspicious because the inscription was notably different from the many known examples of Rubens' hand.
But he said: "Identifying 17th century handwriting is a complicated task. If you're trying to work out these things, the nuances are very subtle. It is the same kind of technique that they use in handwriting in the police force."
In re-evaluating the Chatsworth drawing, every letter of the inscription was closely examined. A sketch book of Van Dyck's, owned by the British Museum, was used as the first point of comparison.
In addition, Mr Royalton-Kisch claimed the style of the two artists' drawings was quite distinct. Whereas Van Dyck was very precise, Rubens tended to be more flowing. This could be seen in the other two drawings now being claimed as Van Dyck's, he said. The first is another depiction, in black chalk, of the dead tree at Chatsworth. The other, of a fallen tree, is a large work held by the Louvre in Paris which he described as "one of the most incredible drawings in the history of paintings from nature".
Arnont Barlis, of the Rubenianum centre for the study of Rubens in Antwerp, and Kathlijne van der Stighelen of Leuven University, two of the half dozen acknowledged world experts in these two painters, have seen the research and support the new attributions.
The significance lies in what this reveals about the early work of Van Dyck, the 400th anniversary of whose birth is being celebrated in exhibitions in Belgium and London this year.
Van Dyck is known to have been an accomplished painter by the age of 14 but these three drawings, if they are really his, are the only ones in existence from his late teens when he was working in Rubens' studio.
"The three drawings are quite illuminating about Van Dyck and his style as an artist and a draughtsman at this period. They show the extraordinary facility he had as a young man," Mr Royalton-Kisch said. The drawings are also revealing of the working methods of Rubens, suggesting that he may have delegated more work to his young pupil than previously acknowledged.
Although it was known that his pupils contributed to paintings at his Antwerp workshop, greater involvement by Van Dyck in works previously attributed to Rubens strengthens the impression of a "production line". This contrasts with the widely-accepted 19th century notion of art history as the history of great individuals.
The drawing held by The Louvre was apparently used in preparation for a painting, "A Landscape with a Bear Hunt", which has always been attributed to Rubens. Re-assigning the drawing raises the possibility that Van Dyck contributed to the painting, now in a museum in Dresden.
Mr Royalton-Kisch is also considering a study of a horse in the Uffizi gallery in Florence which may be a preparatory drawing for a painting in Antwerp which has always been regarded as a Rubens. "It will come as a bit of a surprise that Van Dyck was involved with a couple of pictures the status of which has not been questioned before," he said.
Christopher Brown, who organised the Rubens exhibition at the National Gallery and is now director of the Ashmolean Museum in Oxford, said he was very interested in the new research. "The notes made on the Chatsworth drawing are in a handwriting which does not seem to be by Rubens. It's quite hard to find a piece of Van Dyck's handwriting which is exactly the same, but I can see there's a good argument for that particular drawing," he said.
"I'm slightly reluctant to lose the big Louvre drawing (to Van Dyck) because it seems to have the ambition and grandeur we associate with Rubens. But anything that makes you think about these things again is good."