“There are holes in them and… the condoms burst easily,” a Food and Drugs Authority (FDA) spokesman told the BBC.
The condoms were being distributed free as part of an HIV/Aids prevention campaign by the Ghana Health Service.
About 200 million of the faulty condoms are believed to have been imported into the country.
The BBC’s Sammy Darko in the capital, Accra, says the condom packaging is silvery white with a red Aids ribbon incorporated into the design and the words “Be Safe” also in red.
The FDA has issued an alert about their safety.Thomas Amedzro, head of drug enforcement at the FDA, said the condoms had been imported via Kenya from a Chinese manufacturer.
All imported condoms are supposed to be tested by the FDA before distribution, he said.
“Somehow there was a lapse; the batches of the condoms were not submitted as duly required for the appropriate testing to be conducted,” he told the BBC’s Focus on Africa programme.
Anybody using them could be “exposed to sexually transmitted infections or be saddled with unwanted pregnancies”, Mr Amedzro said.
“You may not be able to see the holes with your naked eye but when you look at it under the microscope you can see holes,” he said.
They were also not adequately lubricated, the FDA said.
Our reporter says the health service took delivery of the condoms in February this year, but they arrived in the country in the last quarter of 2012.
“Since the alert went out, a number of individuals and organisations have already reported to us that they have stocks, which we are already retrieving,” Mr Amedzro said.
A publicity campaign was underway to ensure that all the other unsafe condoms were found, he added.
According to UN figures, an estimated 230,000 people in Ghana, which has a population of 25 million, are living with HIV.