A law change last year allowed these standards to be regulated and enforced.
The ministry (MPI) was now seeking feedback on these regulations and possible penalties for infringements.
It said fines would be introduced for low-level offending, and penalties of between $300 and $500 were likely.
Among the proposed regulations are:
• Dogs travelling on the back of vehicles on public roads must be secured so they do not fall off.
• Pain relief must be given when dehorning cattle, sheep or goats.
• Dog owners may be fined if the animal shows signs of heat distress after being left in a car.
• De-clawing cats and de-barking dogs will be banned unless for therapeutic purposes.
• Horses cannot be whipped around the head.
• Hot branding of any animal will be banned.
• Layer hens must have able to express "normal behaviours" such as nesting and perching and young hens cannot be put in pens smaller than 370 sq cm
There are also specific regulations for the treatment of bobby calves, an issue which came into the spotlight last year after animal welfare activists took out advertisements in British newspapers which showed abuse of young calves on New Zealand farms.
If the proposals went ahead, calves would have to be fed more regularly and handled properly.
Maximum travel times in trucks would be reduced and transport across the Cook Strait would be banned altogether.
There is a separate set of proposals for live animal exports, which has also been a hot issue in the last few years because of mass shipments of up to 50,000 cattle at once.
MPI's director-general of health could be able to ask for reports of the welfare of animals during and after export, and take those reports into account when considering future export approvals.
For more serious offences, individuals could be fined between $5000 and $50,000 or serve jail time.
A new offence of wilful mistreatment of an animal will have a maximum penalty of five years' jail.
Mr Guy said New Zealand's animal welfare system was already considered one of the best in the world.
"The proposed regulations will further strengthen our reputation as a country that cares for animals," he said.
Around two-thirds of New Zealanders owned a pet, and animal products were worth around $23 billion in exports each year.