Some Canadian chartered banks have recently stopped accepting cheques for payment of thirdparty bills (such as property taxes and utilities). They require such payments to be made electronically.
However, section 229 of the Income Tax Act provides:
A chartered bank in Canada shall receive for deposit, without any charge for discount or commission, any cheque made payable to the Receiver General in payment of tax, interest or penalty imposed by this Act, whether drawn on the bank receiving the cheque or on any other chartered bank in Canada.
This means that your bank cannot legally refuse to accept, without charge, a cheque that you provide for payment of an income tax instalment or debt. In practice, GST/HST remittances are also accepted by the banks.