His comments are in conflict with Nigeria's views which has often complained about trade imbalances.
"We know the balance of trade is skewed in favour of Nigeria because of the amount of oil South Africa imports from Nigeria," Motlanthe said.
He was addressing a gathering of local and Nigerian businesspeople.
"We would like to bring parity in this area by improving the trade flows between our two countries," he added.
Nigerian Vice-President Goodluck Jonathan told the same gathering that trade with South Africa was unfairly tilted in favour of the latter.
He said bilateral relations have yielded enormous benefits for South African entrepreneurs with investment in Nigeria. He added that there were few or no opportunities for Nigerians to do real business in South Africa.
"Some Nigerians have questioned the very rationale for the relationship if our relations and the benefits they confer are so skewed," he said.
"And South African authorities are engaged in alleged acts of discrimination against Nigerian visitors, residents and businesses in South Africa."
More than 100 South African companies operate in Nigeria, a jump from only four before 1999. The largest of them are in banking, telecommunications, retail as well as the entertainment business.
No figures of Nigerian outfits that have set up shop in South Africa were readily available.
South Africa, one of the continent's largest oil consumers, gets most of its crude requirements from the Middle East. Nigeria is one of Africa's two top oil producers.
The two countries were scheduled to sign an agreement that is expected to ease immigration problems between their nationals.
But Motlanthe said the deal would have to be deferred to allow for the completion of an ongoing review of South African immigration laws.
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VinceRSA