The business case was updated earlier this year to include expanded plans for the programme since it was first approved by Government in 2013.
"We've done a lot more work with research and sector partners to expand the scope of innovation hubs," AgResearch chief executive Tom Richardson said.
"This has resulted in more ambitious plans with a wider range of partners and increased the scope of our building plans."
AgResearch would self-fund the programme through cash reserves, asset sales and debt.
Science and Innovation Minister Steven Joyce said ministers had made clear their expectations that AgResearch implement the business case successfully.
"It is also our expectation that AgResearch will consult ministers further in advance of key construction commitments for both the Palmerston North and Lincoln building projects."
The approval follows a major shake-up at AgResearch last year that resulted in 78 jobs being axed - the bulk of them from Grasslands.