Nearly two thirds of trusts failed to hit the government's MRSA target, the Liberal Democrats have claimed.
The party compared infection rates for 2007-08 with 2003-04, to see whether the target to halve MRSA rates by March 2008 had been hit.
Their figures contradict official statistics released in July, when the government announced it was within "touching distance" of the target, calculated using quarterly averages.
The Liberal Democrats said it was fairer to compare annual figures rather than quarterly averages because the baseline was the total number of cases in 2003-04.
Liberal Democrat health adviser Rachel Spring said the government's measurement had been "unexpected" and gave the Department of Health "room for manoeuvre".
"No one's disputing there have been improvements but there's still a long way to go," she said.
Last year's public service agreement target requires that the average annual number of MRSA bacteraemias for 2008-09 to 2010-11 should be less than half the 2003-04 figure.
The comprehensive spending review states: "The total number of cases for each year should be below 3,848 (half the 2003-04 baseline)."
The Liberal Democrats' analysis shows 64 per cent of trusts did not meet the target and in 23 trusts MRSA rates rose.
In January, opposition parties accused the DH of moving the deadline for the target to include April to June 2008 figures.
A memo leaked to HSJ last year revealed DH fears that the target was likely to be missed. A spokesman said the target had always been recorded in the same way and needed to use April to June figures to take into account improvements made at the end of March.