"Those involved in the trade have made improvements over recent years, but despite any regulatory measures we could put in place, the voyage times and the journey through the tropics to the northern hemisphere markets will always impose challenges."
O'Connor said the tragic sinking of the Gulf Livestock 1 highlighted the real risks.
"The National Animal Welfare Advisory Committee supported the ban. There are different opinions on its long-term value among farmers, how it affects New Zealand's commitment to animal welfare, and our image in the eyes of international consumers.
He said the impacts on export flow would be small in the context of total primary sector exports.
"Live exports by sea represented approximately 0.6 per cent of primary sector exports last year."
O'Connor also acknowledged those directly affected by these changes but said he believed the two-year transition period provided sufficient time for business models and supply chains to account for the removal of the trade.
"Having said that our commitment to these high standards has already shown its value where animal welfare discussions have been brought up in Free Trade Agreement negotiations with the United Kingdom and the European Union."
The Bill reinforced and built on New Zealand's reputation as a safe and ethical producer of high-quality food products, he said.
"It protects the reputation of not just our farmers now but, the farmers of the future who want to commit to livestock farming assured that we are the best managers of animal welfare and producers of ethical animal protein for the world."