The Government is doubling the time required to stay in New Zealand before returnees can avoid paying MIQ fees.

And it is making it more expensive for some non-Kiwi partners, children or legal guardians to come to New Zealand.

Currently, any New Zealand citizen or permanent resident returning from overseas who has not been in New Zealand since August 11 last year - and who stays here for 90 days - is not liable to pay charges for the $3100 fee for 14 days in MIQ.

From June 1, returnees will need to stay here for at least 180 days.

"This change will support the Government's aim of making the MIQ system more financially sustainable," the Ministry of Business, Innovation and Employment, which runs MIQ, said in a statement.

"It is estimated that extending the minimum period to 180 days will affect about 3 per cent of returning New Zealanders."

The fees will also go up for temporary entry class visa holders who are partners, spouses, legal guardians or children under 18 of returning Kiwis or migrant health workers - if they are travelling separately.

If travelling together, they will pay the lower MIQ additional person rates of $950 for an additional adult in a room, and $475 for a child aged 3-17.

If travelling separately, the temporary entry class visa holder will be charged the higher fees of $5520 for the first or only person in a room, $2990 for an additional adult, and $1610 for an additional child.

This fees increase will take effect from 12.01am tomorrow.

Waivers can still be granted in special circumstances or in cases of financial hardship.