Inland Revenue and ACC will stop receiving cheques as payment from next March.
Inland Revenue said about 5 percent of payments received by it and ACC last year were by cheque.
Deputy commissioner Sharon Thompson said the organisation will help customers switch to other ways to pay.
She said electronic payments are simpler, easier, and safer than cheques.
People will still be able to pay both organisations with cash or eftpos, but only at Westpac banks, and not at ACC or Inland Revenue branches.
In the last financial year Inland Revenue received 430,000 cheques, the biggest number received by any public agency.