Whole Foods Markets Inc has agreed to pay $800,000 after an investigation found that the supermarket chain overcharged customers in California, officials in the state said on Tuesday.

State and local inspectors found during a year-long investigation that Whole Foods charged more than the advertised price on many items, according to a statement from Los Angeles City Attorney Mike Feuer.

Problems included failing to subtract at checkout the weight of salad bar containers, giving less weight than shown on labels for packaged items sold by the pound and selling items such as kebabs and deli foods by the piece rather than by the pound as required by law.

Whole Foods agreed to pay $630,000 in civil penalties to the city attorneys of Los Angeles, San Diego and Santa Monica, who brought the case. It will also pay $100,000 into a consumer protection trust fund, and $68,394 for costs.

The Austin, Texas-based company also agreed to a five-year injunction that requires accurate pricing, increased monitoring of its pricing practices and random audits.

In a statement, Whole Foods said it cooperated with authorities, and that its pricing was accurate 98 per cent of the time.

"We will continue to refine and implement additional processes to minimize such errors going forward," it said.

Whole Foods operates 74 stores in California.