The Chancellor suffered a £5.1 billion black hole after the Office for National Statistics (ONS) said not all of the funds transferred from the Bank of England's economy-boosting programme were allowed to go to government coffers.
It followed the auction of 4G mobile airwaves raising £1.2bn less than had been estimated for the Treasury.
The ONS said the Government recorded a net surplus of £11.4bn last month, excluding interventions such as bank bailouts, compared with a surplus of £6.4bn for January 2012.
Economists fear last month's surplus will not be enough to prevent the Government overshooting its 2012/2013 borrowing target and said the UK remained at risk of losing its AAA debt rating.
However, the pound clawed back some of the ground lost in recent days on fears the Bank will take further action to bolster the economy. Sterling edged up to US $1.53 and was nearly 1% higher at 1.16 euros.
A Treasury spokesman said the public finance figures showed an improving picture, adding they "underline what the Governor of the Bank of England said last week: the road ahead will be difficult, but the economy is on the right track".
Last month's borrowing surplus was helped by a 7% rise in total receipts, up £4.5bn to £65.8bn, with January a strong month for tax returns. Income tax is thought to have been helped by rising employment.