He said staff not receiving the end-of-year sweetener included those in the $100,000-plus pay bracket and the executive team, whose performance bonuses are paid in July.
Asked if he thought the payments were a good look during austere times, Mr Mather said: "It's about doing the right thing.
"Our staff are paid below market rates, we have a low staff turnover and we have a very stable, committed workforce ... I have a view that our staff should also have the opportunity to have their efforts recognised.
"I can see how it creates some negative perceptions but I think it is a smart business decision for Maori Television to be making and I do think our people do deserve its efforts to be recognised."
Maori TV has about 204,000 viewers a day on average, or 0.6 per cent of those aged 5 years and over watching television between 3pm and midnight.
TV One has a 25.2 per cent audience share and TV3 has 14.9 per cent.
Maori Television receives $16.6 million in direct state funding and $16.1 million from Te Mangai Paho.
It also receives about $20 million via the Te Mangai Paho contestable fund, which is paid directly to independent producers.
The station reported a surplus of $775,000 for the last financial year to June 30.
In the money
$78k pot for Maori TV staff bonuses
$500 bonus to majority of staff
$775k funding surplus for station last year