Mr Flavell said the Auditor-General's report had acknowledged the value of the approach.
"At the same time, we can take some valuable lessons from the report and we will do so."
The funding will go to the commissioning agencies responsible for running Whanau Ora in each region.
"They act as brokers for whanau and support them to achieve their goals."
The programme is aimed at taking a more family-wide approach to social services with 'navigators' liaising with Government agencies and families to ensure they access the help they require. It was set up by former Maori Party leader Tariana Turia and began in 2010.
The Budget also included a new funding package of $35 million to establish a Maori Housing Network and liaise with iwi and other Maori housing organisations keen to take part in developing Maori land for housing and provide social housing.
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The funding includes $5.7 million a year for the Maori Housing Network which will be established on July 1 and fund regional housing facilitators in a support role and to address housing shortages among MaoriIt is in addition to the $28 million allocated in previous years to improve housing on Maori land by helping pay for infrastructure.
The new group will help iwi interested in taking part in the Government's plans to sell off state housing and public land and using social housing groups more. Mr Flavell said it was important for Maori to have access to safe, healthy homes and the Maori Housing Strategy was aimed at helping that.
It follows news that John Tamihere's Te Whanau O Waipareira Trust hopes to enter Auckland's housing market to provide affordable housing within the city. The trust is bidding on two large blocks of state land in Massey, and looking for a role building apartments on top of The Warehouse in Newmarket but wants to do in partnership with the Government or private corporates.
Other Maori Budget initiatives:
• $2.1 million for a suicide prevention programme targeting Maori youth. Mr Flavell said it would link in with the Whanau Ora programme. Suicide rates for young Maori were almost double those of non Maori.
• $12.8 million for a new Te Ture Whenua Maori Network to help Maori land owners improve the productivity of their land, targeting areas such as Northland, East Coast, Bay of Plenty, Manawatu, and Whanganui. Mr Flavell said large tracts of Maori land was underutilised and improving its productivity would benefit the owners and the wider.
Live coverage and analysis of Budget 2015 from 2pm on iHeart Radio