Federated Farmers rural security spokesman Miles Anderson said this would be impractical and ineffective, and could lead to an explosion in pests.
"Pests don't wait for pest-control contractors to turn up," Anderson said.
"A farmer might just come across these species in day-to-day business and need to deal with them there and then. It's just not practical for farmers to get contractors in to do the work.
"It's the equivalent of asking us to paint the Auckland Harbour Bridge with a toothbrush."
The bill amounted to calling farmers untrustworthy, he said.
Nash said bowing to Federated Farmers would have opened a large loophole.
"There is no doubt in the South Island that we have a pest problem. That's why we've given an exemption to licenced and registered pest control organisations to go out and shoot these things.
"If a group of farmers want to get together and perhaps form a pest-control business themselves, there's nothing from stopping them from doing that."
In the bill's second reading today, Nash cited the submission of Rural Women NZ, whose spokeswoman Angela McLeod told the committee last week: "If there is a perceived need for semi-automatic firearms, then the shooter needs to learn how to shoot."
Anderson criticised Nash's comments about farmers setting up their own business as a "simplistic and naive response".
He said a farmer could store a firearm at least as safely as a pest-control contractor with a firearm in their vehicle.
"Which is the greater risk? We're not asking for a blanket exemption, only where there is a genuine need."
Conservation Minister Eugenie Sage said Federated Farmers' wishes would have undermined the purpose of the bill.
"We want to ensure we ban semi-automatic weapons. They have got no place in New Zealand.
"The 16,0000 people would have potentially been able to have semi-automatic weapons if Federated Farmers' views had prevailed."
National Party police spokesman Chris Bishop also backed up the committee report, saying it struck the right balance in making New Zealand safer and not unduly punishing gun owners.
The bill passed its second reading with the support of all parties except for Act.
It will pass the remainder of its legislative stages tomorrow, receive the Royal Assent on Thursday, and is expected to be in force on Friday.