RICHMOND -- The holder of one of the city's six permits to sell medical marijuana agreed Thursday to pay about $62,000 in back fees as he continues to look for a place to open up shop.

John Valdez, owner of Richmond Compassionate Care Collective, has been searching for a spot for more than two years. Most recently, he was thwarted in his effort to open a site in the Santa Fe neighborhood after an outpouring of residents persuaded the City Council to reject his application by a 4-2 vote in July.

Police Chief Chris Magnus initially recommended revocation in his presentation to the city's Public Safety Commission on Thursday but brokered a deal with Valdez and his lawyer to accept the back fees within 10 days and give him another six months to open a shop.

"The city is losing substantial revenue by not receiving the permit fees nor the 5 percent sales tax," Magnus said.

The three-member committee agreed to the terms to allow Valdez to hold the permit.

The city in 2010 granted three permits for dispensaries, then doubled that to six in 2012, making it the Bay Area's most dispensary-friendly city per capita. But permit holders have faced a number of hurdles, including community opposition to new shops and zoning ordinances that limit them to just a few areas in the city, and not near schools and residences.

Today, only three of six original permit holders are operating dispensaries in the city, Magnus said. Two permits have been revoked and will be open to new applicants later this year.

Holding a permit carries significant costs. Permit holders must pay the city $15,690 quarterly, Magnus said, and pay 5 percent of all revenues in tax, in addition to other standard business taxes. Valdez stopped paying his quarterly fees after his setback in July.

Valdez's attorney, James Anthony, told the committee his client was confident he would be able to find a spot to open his business now that "a more tolerant" atmosphere toward medical marijuana dispensaries appears to have taken hold.

Since voters approved Proposition 215 in 1996 to legalize medical marijuana, the movement toward easing restrictions has played out on a city-by-city basis. While cities such as Berkeley, Oakland and San Francisco have dispensaries, many others have enacted bans, thanks in part to a state Supreme Court ruling that affirmed the right of local governments to restrict them.

But Anthony said the trend is toward a more hospitable atmosphere for dispensaries.

"More financing and more leasing options are available now," Anthony said, adding that federal enforcement of anti-marijuana laws has waned in recent years. Contact Robert Rogers at 510-262-2726. Follow him at Twitter.com/sfbaynewsrogers.