A damning report has criticised the Chief Electoral Officer for "poor planning, insufficient communication and the lack of an overall management plan" during last May's elections.
The criticism comes in a report from the Electoral Commission, a UK-wide standards body.
The May 5 count caused massive frustration among politicians and the public after it took two days to complete.
The first result, from South Armagh, did not come in until 7pm the day after polling when 3pm would have been normal.
At the time Mr Shields blamed the fact that council and Assembly elections were held on the same day as an STV referendum.
Last night Seamus Magee, the head of the Electoral Commission's Belfast Office, said Mr Shields had had adequate staff and resources to handle the challenge.
"The real difficulty was that there was no overall management plan for the count. Though planning went well in the run-up to polling day it all seemed to fall apart at the count," he said.
The report calls for the Northern Ireland Electoral Office to be included in legislation which allows performance standards to be compared with other UK regions. At present it is the only region excluded from the scheme.
"We want the Electoral Administration Act extended to Northern Ireland because we currently have no measure of how good or bad electoral administration is here. There is no direct comparator. Effectively the Electoral Office sets its own standards in conjunction with the Northern Ireland Office," Mr Magee said.
Last night an NIO spokesman said that ministers were considering the change, as was Mr Shields.
While his report says the election and registration process was run well, Mr Magee paints a shambolic picture from close of polls until the votes were verified.
"About 30% of presiding officers got their electoral accounts wrong," he said. "The documentation was mixed in with rubbish and that was all sent to the count centres where it took a hell of a long time to sort out. That led to long delays."
In Ballymena, Assembly and referendum votes were mixed up and in Omagh some ballot papers had to be dried out with hairdryers.
Mr Shields and other senior staff didn't turn up at a UK wide rehearsal for the referendum count citing a threatened judicial review of a council nomination.
"It was very unfortunate that the CEO wasn't able to turn up and take control," Mr Magee said.
He added: "He didn't communicate effectively to those who were managing the referendum count what it was they were supposed to be doing."
The report also found that Area Returning Officers were forced to work excessive hours training 6,000 part-time staff in the run-up to the election and then manage eight count centres.
This caused delays because they were too tired.
"There should be a split between staff working on polling day and at the count," Mr Magee said, adding that there had been sufficient staff to do this.
To make matters worse, 108 part-time staff didn't turn up or dropped out before the count.
The report makes 30 recommendations.
Mr Magee said it did not imply that Mr Shields should resign.
"Polling itself went exceptionally well.
"The elements that didn't work well were the referendum and elections counts.
"I think it is fixable with hard work and assistance from the Electoral Commission."
Mr Shields is now conducting his own review which he said had already adopted many of the Electoral Commission's recommendations.
"I will consider the report carefully and ensure that any learning points are taken forward," he said.
