A total of 23 areas that were due to be audited have been cancelled or deferred to be looked at next year instead.
The list includes adult social care casework, taxi licence fees and the Bolton Vision Strategy and Plan.
The internal auditing team blamed a lack of resources, including higher than anticipated sickness absence and three members of the team leaving the council.
Conservative group leader David Greenhalgh, who chairs the council’s audit committee, was concerned that this is the second year in a row that the deadline has been missed.
He said: “It is of real concern, that after assurances had been given that the audit plan would be completed this year, 23 audit plans have either been cancelled or deferred, and among those, some areas that have previously been in the spotlight and raised national criticism.
“None more so than an internal audit into ‘Grant Payments’. We all remember the debacle over Labour’s award of the grant to Asons. If there was ever a time to regain confidence in a specific area within this council, it is now for the process regarding the award and payment of grants.”
In November 2016, Asons Solicitors in Churchgate received a grant of £300,000 from the council using emergency powers to carry out refurbishment work.
The grant was secretly approved but minutes from a private meeting shown to The Bolton News revealed that then director of place, Stephen Young, and then council leader, Cliff Morris, were behind the agreement.
After an external audit by KMPG, decision to award the grant was found to be “legal” and “appropriate” but the council was criticised for a lack of documentation when using emergency powers.
READ MORE: The Asons Solicitors story so far
Head of internal audit and risk management Tom Powell explained that certain areas have been prioritised and will undergo a risk assessment, while others will be checked in the next financial year.
Following Wednesday’s committee meeting, Labour councillor Sue Haworth said she was not concerned because she had been assured that the system has a lot of due diligence.
But she said the department still needs to prove itself so that the delays do not happen again.
The annual internal audit report, which was approved at the meeting, also revealed the amount of payments that the council made twice in error.
In the last financial quarter, £39,000 of duplicate payments were identified, with a further £42,000 earmarked for recovery.
This came from analysing data from eight out of the 12 core financial systems which also revealed overpayments of £3,000 which are being recovered.
Cllr Greenhalgh raised further concerns about payments not being requested by the council, using an example of a group in his ward.
He said: “Every year that community group has to own up that they haven’t been asked for their payment. People won’t often come forward.”
Crompton councillor Bilkis Ismail asked what systems were in place to prevent duplications and make sure the council gets paid.
The committee was told that there needs to be a culture change and more discipline among council staff who are responsible for requesting individual payments.
The Tory leader also asked the internal audit team to look at payments made as part of the Neighbourhood Management and Area Working fund.
This has recently been in the spotlight as it was revealed that eight wards in the borough received 85 percent of the £2.6m handed out since 2011.
Concerns were raised because a paper trail of how this money is spent was not publicly available even though ward councillors have access to the details.
Cllr Greenhalgh said: “Nobody is saying that anybody is hiding anything. But in every other department amounts are listed. If there’s nothing to hide, then why hide it.”