Arrears were 0.5% greater than in the previous year, and councils lost a further£22m through homes left empty.
Times taken to re-let vacant homes improved slightly compared with the previous year, with 59% let within four weeks in 2003-04, against 65% before.
Only West Lothian Council managed to re-let 90% of vacancies within four weeks, while Aberdeen City Council and West Dunbartonshire Council took more than four weeks over 90% of lettings.
The best performer was Angus Council, with 94.9% within the target, and the worst East Dunbartonshire Council at just 3.5%.
Accounts Commission chair Alastair MacNish said he would be 'looking for improvements'.
There were better performances in social work, where the number of appropriately qualified staff in homes for elderly people rose two percentage points to 41%.
More than 86% of social enquiry reports were allocated to social work staff within the two-day target, a slight improvement on the previous year, and 95% submitted to courts by their due date.
The Convention of Scottish Local Authorities said it had 'taken a strategic decision' not to respond to the latest findings.