Consumer watchdog Which? looked at areas including the number of high and medium-risk food businesses which kept to hygiene standards and the number of interventions that were carried out.
But Birmingham City Council said Which? had failed to engage with local authorities and Hyndburn Council said the data was out of date.
Erewash in Derbyshire was rated top.
Data from 390 local authorities for 2016/17 was used, including information from the Local Authority Monitoring System collected by the Food Standards Agency.
Which? said Birmingham City Council had a poor record for carrying out inspections within 28 days of a food business opening.
It found that 16% of the city’s more than 8,000 food businesses were yet to be rated and 43% of the city’s high and medium-risk food businesses did not meet food compliance standards.
Hyndburn Borough Council in Lancashire was the second worst area in the UK for food hygiene.
Which? said that 98% of the area’s businesses had been rated for risk, but just two in five of its medium and high-risk food businesses met hygiene standards.
Mark Croxford, of Birmingham City Council, said: “I am surprised and disappointed to see Which? have made the same mistake as they have done in previous years, in failing to engage with local authorities to produce a meaningful report.”
He said that the same data showed council officers had inspected the second highest number of premises, undertaken more prosecutions, closed more food premises and suspended more approved manufacturers than any other English local authority in 2016/17.
Mr Croxford said more than 1,000 new food businesses were registered in Birmingham in 2016/17, presenting a “significant challenge”.
He added that the council’s officers have 8,341 premises to inspect across Birmingham – second only to Cornwall with 8,652.
Hyndburn Council’s deputy leader Paul Cox said the findings were “not a true reflection of the current picture in Hyndburn”, saying the statistics used were 13 months out of date.
He said “significant strides” had been taken to improve food hygiene performance and there had been a “big improvement”.
“We’ve completed 100% of inspections for the past two years and our most recently submitted figures to the FSA for 17/18 shows the true picture that 92.5% of food businesses in Hyndburn are compliant,” he said.
Erewash Borough Council was rated top for the second year in a row, ahead of Basingstoke and Deane Borough Council in Hampshire.
The top 10 local authorities
- Basingstoke and Deane
- North Dorset
- South Kesteven
- West Dorset
- Staffordshire and Moorlands
- Orkney Islands
The bottom 10 local authorities
- Isles of Scilly
- Waltham Forest
Alex Neill, of Which?, said the UK’s enforcement regime was “under huge strain, just as Brexit threatens to add to the responsibilities of struggling local authorities”.
“Effective food enforcement must be a government priority, including robust checks on imports as well as co-operation with the EU and other countries on food risks.”
Councillor Simon Blackburn, chairman of the Local Government Association’s safer and stronger communities board, said councils worked “extremely hard” to maintain and improve food hygiene standards.
“Ultimately it is the responsibility of food businesses to ensure the products they produce and premises they serve from comply fully with food safety law and pose no risk, but councils continue to do everything possible to maintain checks in this area despite severe budgetary pressures,” he said.