Angela Smith, the Minister for the Third Sector, overclaimed a total of £1,429 of expenses, according to the final report into MPs' claims published by auditor Sir Thomas Legg.
In June last year, the MP for Basildon repaid more than £1,000 in wrongly claimed council tax expenses and service charges for her second home, a flat in London's Elephant & Castle.
In December, Smith said she had paid back a further £300 Legg had asked her for. But Legg's latest report says she still owes £396 of the £1,429.
However, a spokesman at Smith's constituency office said she had paid back the full amount in December, but Legg's figures had not been updated to reflect this.
Two former third sector ministers, Phil Hope and Paul Goggins, have made repayments worth thousands more than the Legg report required. Hope took out a loan last year to repay £42,674, the highest so far of any MP, but has now been told he owed only £4,365. Goggins repaid £21,307, but has been told he owed only £1,076.