The clothing racks and walls are lined with vintage wear. Colorful shirts, pants, jackets, dresses, accessories and more pack the store. But just days before Flamingos Vintage Pound was set to open in the former Rasputin Music location in the Haight-Ashbury neighborhood, the shop was informed by the city that it could not.

Flamingos, a Spanish retailer, had hoped to open at 1672 Haight St. on Dec. 6, but now, brown paper covers the windows of the building, recently painted with the shop’s sign and bright pink and turquoise company colors. A fully stocked but closed store sits — with an opening postponed for what could be months.

“We are devastated,” owner Daniel Martinez said in an email. “What’s worse is that this seems to be a lengthy process and we cannot afford months of paying rent with a closed business.”

The issue is that Flamingos is considered a chain store. That’s because it has more than 11 locations worldwide, even though there are none in San Francisco. The city requires all chain stores to go through a permit process known as conditional use authorization. That permit is usually required when the use of a space is changing, like a retail site becoming a restaurant, but chain stores must get one regardless of what they replace.

Chain stores are allowed on Haight Street, unlike shopping hubs in Hayes Valley, Chinatown and North Beach. (The Haight Street area bans chain restaurants, however.)

A spokeswoman from the Planning Department said the conditional use application process takes “no less than 6 months but it often depends on the number of other conditional use applications pending.”

Martinez said he did not know about the permit requirement for chain stores in San Francisco and he’s worried because he’s still on the hook for rent. He declined to comment on contract terms but said his lease in the Haight was “for more than a year.”

“I’m not American, and nobody told us anything, I think it is impossible to know all the local laws of all the United States,” he said. “We have lost hundreds of thousands of dollars for not being able to open this business.”

Martinez founded the company in 2009 in Spain. It has more than 30 locations across Europe, Asia and the U.S., including in Los Angeles, Miami and Austin, Texas.

As in other neighborhoods, including North Beach and the Bayview, shops in the Haight are struggling amid the rise of e-commerce, and coping with high rents, the need for seismic retrofits and the difficulty of navigating city bureaucracy. The Haight has at least nine empty stores (including Flamingos) as of mid-December, down from 15 this summer, based on an informal Chronicle count that does not include side streets. The Haight Ashbury Music Center closed recently, and long-standing vacancies include the former locations of 4 Kids Clothing and Haight Street Shoe Repair, both empty since 2015.

The Haight Street Merchant’s Association said the Flamingos situation could have been avoided.

“All businesses should play by the rules,” said Christin Evans, president of the Haight’s merchant association and owner of the Booksmith. “But we could have avoided a shut store. Rasputin’s didn’t have to close, they could have stayed open while Flamingos figured out the permitting process.”

Ken Sarachan, the landlord of the property, founded Rasputin Music in Berkeley in 1971, and closed the store in early November. He did not respond to requests for comment.

Evans said the merchants association is not opposed to chains. Another vintage clothing retailer, Japan’s 2nd Street, is currently awaiting its conditional use permit to open in the neighborhood.

People sometimes loiter in front of empty stores, making shoppers uncomfortable, according to Sandra Murphy, store manager at My Favorite, a gift shop next to Flamingos.

“It’s unfortunate,” she said. “It doesn’t just affect us, but it impacts business on the whole street.”

Martinez said he respects and understands the laws, but comparing his company “with multimillion-dollar corporations like McDonald’s that can go through this type of process does not make much sense.”

“A space on Haight Street not open for business does not benefit anyone in the area,” Martinez said.

Shwanika Narayan is a San Francisco Chronicle staff writer. Email: shwanika.narayan@sfchronicle.com Twitter: @shwanika