Last November, Action Medical Research used the Freedom of Information Act to determine how much the Government had spent on premature birth research in 2004/05.
It published the results in a press release that showed £3.7m - 0.3 per cent of the total medical research budget for that year - went on studies into premature babies.
The DoH publicly refuted the charity's claims, stating the actual total was nearly double the figure quoted.
Action Medical Research filed a second request under the Freedom of Information Act to determine which sum was correct.
The charity received a written and verbal apology from the DoH this month, saying it had made a mistake and the original £3.7m figure was accurate.
"The mistake came about because, in preparing our press statement, we drew on material connected with an earlier enquiry about research into premature birth," said Colin McDonald, freedom of information officer at the DoH. "We had no intention to mislead."
A spokesman for Action Medical Research said the charity was pleased with the victory, but the figure remained too low. "Whether it's £3.7m or £6m, these figures are still pitifully low," he said. "We consider this a national emergency."
The charity is now asking supporters to send in their photographs and stories of premature birth for a book it intends to send to Patricia Hewitt, the health minister, and Lord Hunt, the minister in charge of research budgets at the DoH.