SAO PAULO (Reuters) - Government-controlled Banco de Brasilia (BRB) only agreed to acquire the healthiest and most strategically relevant assets from fellow lender Banco Master after months of negotiations, BRB CEO Paulo Henrique Costa said in a Tuesday interview.

The agreement, announced on Friday and subject to review by the central bank, is still under due diligence that could eventually bring down the negotiated price of 2 billion reais ($350 million), to be paid over up to six years, he added.

Shares of BRB, which is controlled by the government of Brazil's Federal District, have nearly doubled on news of the deal. However, the lack of prior regulatory approval has spurred questions about the future of Banco Master's remaining assets.

Master had pursued an aggressive growth strategy funded by high-yield certificates of deposit and heavy capital allocation in assets backed by court-ordered government payments called "precatorios."

Costa said BRB has only selected assets aligned with its current strategy of expanding its client base and core business, excluding assets involving court-ordered payments and investment funds containing company shares.

That left about 23 billion reais of assets outside the deal with Master, under negotiation since January, he said.

"This was one of the conditions of our contract," Costa said in a telephone interview.

Heavyweight Brazilian investment bank BTG Pactual has shown interest in some of the Banco Master assets that BRB passed over, according to a person familiar with the matter.

Costa said that he has not taken part in any discussions about what Banco Master's controlling shareholder Daniel Vorcaro aims to do with the leftover assets after BRB acquires 58% of its capital.

"The other 42% belongs to Daniel, of course. Whether he will carry this in the future or not, these are elements that I don't have," said Costa.

He said BRB informed the central bank of the agreed transaction on Friday and presented related documents at a meeting in Brasilia on Monday night.

The regulator now has 360 days to make a decision, but Costa said he expects approval likely to come sooner.