The Food and Drug Administration (FDA) said six cases in 6.8 million doses had been reported and it was acting "out of an abundance of caution".
Following the news, South Africa, the first country to use the jab, said it would suspend its rollout.
Johnson & Johnson said it would also delay its vaccine drive in Europe.
The US move follows similar rare cases in the AstraZeneca vaccine, which has prompted some curbs in its use.
Dr Anthony Fauci, the top Covid adviser in the US, said it was too early to comment on whether the vaccine could have its authorisation revoked.
The US has by far the most confirmed cases of Covid-19 - more than 31 million - with more than 562,000 deaths, another world high.
The picture for the virus there is complicated, though, with some areas in the north seeing surges in infections, the south less, and with the figures not always reflecting inoculation numbers.
The Johnson & Johnson jab was approved in the US on 27 February and its use has been more limited so far than that of the Pfizer-BioNTech and Moderna doses.
Nevertheless, the government had hoped for hundreds of thousands of vaccinations of the jab every week. Unlike some of the other vaccines, it is dispensed as a single shot and is stored at common refrigerator temperatures, making it easier to distribute.
In South Africa, studies showed the Johnson & Johnson vaccine had a higher protection rate against the South African variant than other jabs, and since mid-February, nearly 300,000 healthcare workers have received it.
There have been no cases of blood clotting in South Africa, but as a precaution, the rollout has been temporarily suspended there, Health Minister Zweli Mkhize confirmed. The country has secured an additional 10 million Pfizer vaccines, he added.
The Johnson & Johnson vaccine is also known as the Janssen vaccine, named after the Belgian company that makes it.
The jab was approved by the European Union last month, and this week the first doses started arriving in the bloc. In a statement, the European Medicines Agency (EMA) said it is continuing with a safety review that began last week, but said there is no clear link between the vaccine and the blood clots.
The EU's vaccine roll-out has been criticised by the WHO for being too slow, and there are concerns this latest delay could throw it into further turmoil.
The Johnson & Johnson vaccine is yet to be approved in the UK, although 30 million doses are on pre-order. The Department of Health said the rollout delay would not affect vaccine supplies in the UK, or derail the aim to offer a jab to all adults by the end of July.