The investment would also pay for breeding programmes, research, and expansion of DoC predator control programmes.
Kiwis for Kiwi welcomed the boost but said extra funding from other sources was needed to save the kiwi.
The Budget also came with new funding to help ease in law overhauls, including $20.4 million to help councils with proposed changes to the Resource Management Act, and $4 million to help the Environment Protection Authority to administer new legislation for the country's Exclusive Economic Zone.
Environmental Defence Society chairman Gary Taylor said although the kiwi management funding would have wider benefits for biodiversity, he expected the decline in land, freshwater and marine domains would continue.
But despite a slight drop in overall DoC funding he saw the Budget as "reasonable" for conservation and slightly better for environment.
"However, with the projected surplus in 2016-17, we will be looking for a much larger conservation dividend to help turn around continuing species loss in New Zealand."
Forest and Bird was pleased to see extra funding for 1080 pest control, but remained concerned about DoC's capacity to deal with another plague-producing beech mast (seed production) season.
Raglan environmentalist Phil McCabe, who spelled out his Budget hopes in the Herald this week, said it was "disheartening" to see no new packages specially aimed at marine conservation.
Support for kiwi welcomedEnvironment highlights:
• $41.2 million in new funding for environmental priorities.
• $11.2 million over four years to help save the kiwi.
• $20.4 million over four years to help guide councils on Resource Management Act changes.