David Benson-Pope and Steve Walker had been in line for a base remuneration rate of $64,353, but the Remuneration Authority noted this would have amounted to a pay cut for councillors without extra responsibilities.
They might now both get $8430 more than had been proposed in October.
All other councillors — those who chair committees and their deputies — can expect to have their proposed pay increases reined in a little.
The authority did not accept the council’s proposal for allocating total pay of $1,191,826 among councillors.
Councillors will next week consider a revised allocation proposal to put in front of the authority.
It has been indicated the authority would accept the revised proposal.
Cr Walker said he was encouraged the Remuneration Authority "recognised the overly punitive treatment of myself and Cr Benson-Pope and rectified the situation by not approving the proposed allocation".
Remuneration emerged as an issue for the new council when this was debated at the inaugural meeting in October.
When the election was over and after discussions with councillors, new Dunedin Mayor Jules Radich allocated roles to them, including who would chair committees or deputise.
Crs Walker and Benson-Pope were missing from the list and Cr Walker has said the mayor offered deputy roles "he knew we’d decline".
When councillor pay was discussed at the October meeting, Cr Marie Laufiso proposed a structure that would have eliminated the gap between councillors with deputising roles and those without.
Her alternative proposed pay scale — supported by Crs Walker, Benson-Pope and Christine Garey — was voted down, 11-4.
The new proposed pay scale would result in deputy mayor Sophie Barker having her remuneration trimmed from what had been proposed in October by $2144 to $110,475.
Councillors chairing committees would each lose $403 from the earlier proposal, and would now get $90,979.
Councillors with deputy roles would each get $77,982 ($2460 less than previously proposed) and those without such responsibilities would receive $72,783.
The mayor’s remuneration is determined separately.
