“It’s been very frustrating,” Mr. Kaner said in an interview last week at his office in the Bronx, the home of his family-owned business. He bought most of the equipment he needed before Oct. 1, he said, and has been waiting months to get it certified. The delay, he said, pointing to a tall pile of paperwork, has cost him thousands of dollars in payments for fraudulent purchases.

“There’s no recourse,” Mr. Kaner said.

The long delays are just the latest black eye for the deployment of the new systems. Some consumers have not yet received new cards. Many merchants have not bought the updated equipment. And even when the cards and the terminals have been updated, they have generated confusion and slow lines.

Many of the complications were widely predicted, but the certification system has added an unexpected wrinkle — and lots of finger-pointing.

Banks say that retailers waited till the last minute to update their terminals. Retailers point to financial ties between the banks and the companies that provide certification, saying there is no motivation to move faster.

“I think there are merchants who should have been prepared and aren’t,” said Thad Peterson, a senior analyst with the research firm Aite Group. “I think there are merchants who thought they were prepared but aren’t.”