Nearly all twins are either fraternal - in which two eggs and two sperm create two separate embryos, or identical - in which one embryo is fertilised by one sperm and splits into two embryos.
The twins were discovered to be semi-identical while their mother was still pregnant.
Nicholas Fisk of the University of New South Wales Sydney, who led the team behind the find, said: "It is likely the mother's egg was fertilised simultaneously by two of the father's..."
Fraternal twins happen when two different sperm cells fertilize two different eggs, creating two different zygotes, both of which end up implanted in the uterus as developing embryos.
The twins are from Queensland, Australia and genetic testing revealed they were identical on the mother's side, but only have part of their father's DNA.
Experts at the Queensland University of Technology said, after fertilisation, the egg split into three embryos with DNA from two sperm.
Identical - or monozygotic - twins pop up from a single fertilized egg that eventually splits in two and forms two identical boys or two girls.
On average, 75 per cent of semi-identical twins' DNA will be identical as a result.
We all know a set of twins; perhaps even a set of identical twins.
The identity of the twins has not been revealed. According to a press statement about the research, the twins are only the second set of semi-identical twins ever reported in the world, and the very first set to be identified while still in utero.
The now four-year-old boy and girl twins share 100% of their mother's genes, but are like siblings on their father's side, sharing a proportion of their father's DNA.
Doctors in Australia say they have identified a second case of twins apparently created from one egg and two sperm, a boy-girl combination in whom the mother's DNA is identical in both babies but the father's DNA varies in each twin.
To test whether the phenomenon might be more common than doctors believed, Dr Gabbett's team examined an global database of 968 fraternal twins and their parents, but none showed the same pattern. But when the woman came in for a follow-up ultrasound at 14 weeks, it was discovered that she was carrying a boy and a girl-something that is impossible in identical twins.
The only other reported instance of sesquizygotic twins was identified in the United States in 2007. Doctors identified them when one baby had ambiguous sex organs.
The case was shared in a paper in the New England Journal of Medicine on Thursday.
"Otherwise", Gabbett said, "the two twins are lovely kids, well and healthy".
"Three sets of chromosomes are typically incompatible with life and embryos do not usually survive", he said.
The authors also performed genetic tests of 968 sets of other twins presumed to be fraternal to see if any were really semi-identical.