Landcorp has apologised to Associate State Owned Enterprises Minister Shane Jones for not letting him know it was submitting to the Tax Working Group.
The Tax Working Group is examining the structure, fairness and balance of New Zealand's tax system.
Landcorp, the government-owned farming enterprise, made the submission a month late due to a series of internal factors, including a bereavement.
The Tax Working Group accepted Landcorp's submission anyway, which talks of the agriculture sector needing to take a strong lead on reducing New Zealand's environmental footprint.
National's agriculture spokesperson Nathan Guy said Landcorp must have been told to submit as it was advocating for a water tax, nitrogen fertiliser tax and was not opposed to a capital gains tax in its submission.
"They've obviously been leaned on. This government wants to bring in environmental taxes. They want to tax the hell out of hardworking farmers in New Zealand."
But a spokesperson for Mr Jones rejected that, saying he was not even aware a submission had been made until it was reported by media on 28 November.
Submissions closed at the end of April, with Landcorp's offering received by the working group in May.
Landcorp, being a state-owned enterprise, is required to inform the minister of matters that may be of interest.
In this case it failed to flag the submission, and said in a statement that it regreted that.
But it said it was important Landcorp contributed to ongoing debate about environmental taxes, land taxes and capital gains taxes - all of which had an impact on its operations.
"We recognise with our size and Crown ownership that we have an obligation to be actively involved in the discussion around these important issues," the statement read.