Whole Foods has agreed to pay $500,000 to settle accusations by New York authorities that it routinely overcharged customers.

The city’s Department for Consumer Affairs (DCA) said the upmarket grocery chain had to meet standards on weighing and labeling.

The deal means customers “are better protected from overcharging”, it said.

Whole Foods admitted to making mistakes but said there was “no evidence of systematic or intentional misconduct”.

The natural foods and organic retailer said it agreed to the settlement, which was below the $1.5 million originally demanded by the DCA, “to put this issue behind us so that we can continue to focus our attention on providing NYC customers with the highest level of quality and service”.

The DCA first accused Whole Foods in June after an investigation found mislabeled weights on 80 types of pre-packaged products it tested.

Whole Foods was said to have overstated weights of pre-packaged meat, dairy and baked products.

In 2014, Whole Foods agreed to pay $800,000 in penalties and improve pricing accuracy after a separate investigation into alleged pricing irregularities in California.