On 12 September, 43 sheep were put down after a lorry was stopped at the port, and two more died in another incident.
"Exporting animals is a legal trade," Peter Garbutt, the NFU's chief livestock adviser, said.
But Thanet District Council, which imposed the ban, said construction work was needed before any resumption.
"The health and welfare of the animals through transit is the top priority of farmers."
Thanet District Council suspended live exports through the Port of Ramsgate on 20 September and live animals were sent abroad from the Port of Ipswich.
Mr Garbutt said anyone transporting animals had a duty to use the shortest route to reach their destination.
"We have made it clear that the port of Dover would be the most suitable location, but as the boat being used is unable to dock there currently, Ramsgate is the next best option available," he explained.
Thanet council said that live exports had been "suspended until further notice" and its lifting would depend on the construction of "suitable facilities" at the port.
Live animal exports have been suspended from the Port of Ipswich, a week after sheep were sent overseas.
RSPCA chief executive Gavin Grant said: "ABP [Associated British Ports] have acknowledged to the RSPCA that, like Ramsgate, their port did not have suitable facilities to help the animals should an emergency arise."
The 43 sheep that were destroyed were examined by vets who found that one had a broken leg, another was so sick it had to be put down, and 41 were severely lame.
None of the animals could reach their drinkers in the vehicle, the RSPCA said.
Six sheep fell in the water while being taken off the lorry, and four were rescued by RSPCA officers, but two drowned.
In another accident, two sheep died when a loading area floor collapsed as the livestock was being taken off a lorry.
Live animal exports need to resume from the Port of Ramsgate following their suspension after the death of 45 sheep, the National Farmers' Union says.