Environment minister Caroline Spelman told a press briefing that "everyone has to take their cuts. We have discussed it with Kew and they will have to manage that."
The size of the cuts have not been finalised but the projects budget is understood to be unaffected.
"I hope Kew will look at how it can enhance its own income. It has its opportunities to generate income.
However she said the Millenium Seedbank would get an extra £3 million funding.
This was because the initial Millenium funding stream was due to run out shortly and unlike Kew the Millenium Seedbank did not have so many ways of generating its own income.
Overall the department has had to make 30% of savings which will mean between 5000-8000 job losses from its total roll call of 30,000.