A pair of rating agencies is keeping its eyes on three Berkshire Hathaway subsidiaries as the company looks to acquire a majority share in the Burlington Northern Santa Fe railroad.

Fitch Ratings put Berkshire Hathaway, as well as its National Indemnity Group, GEICO and Gen Re subsidiaries, on “rating watch negative,” and A.M. Best put the subsidiaries under review with negative implications.

The financial strength ratings (FSR) of A++ and issuer credit ratings of “aaa” for Omaha, Neb.-based National Indemnity, Chevy Chase, Md.-based GEICO and Gen Re, domiciled in Delaware, were all put under review by A.M. Best.

The moves come after Berkshire Hathaway announced its intent to acquire the outstanding shares of Northern Santa Fe Corp., increasing its holdings to 100%. The transaction is valued at $44 billion and includes the assumption of $10 billion of the railroad’s debt.

Both Fitch and A.M. Best noted their concerns about the purchase, notably Berkshire’s asset profile and capitalization.

Fitch said it viewed the potential transaction, expected to close in the first quarter of 2010, “as increasingly shifting the company’s asset profile toward concentrated investments in operating subsidiaries that use more financial leverage and often have greater sensitivity to general economic conditions than the company’s long-held insurance and holding-company equity oriented investments,” according to press reports.

A.M. Best’s concerns regarded the use of Berkshire Hathaway’s insurance and reinsurance operations as a funding source for the deal, according to a statement.

The latter ratings service also noted its concern with the liquidity and concentration risk of “a single large investment” as a substantial portion of the company’s portfolio, “since the majority of [Berkshire Hathaway’s] equity investments are held at the insurance and reinsurance entities.

“A.M. Best will assess the under review status over the near term as more details regarding the capitalization and liquidity of the insurance and reinsurance operations is presented by management,” it said.