The 57.98 million-share, or roughly 10.8 percent, stake was revealed in a Friday night filing with the U.S. Securities and Exchange Commission. Phillips 66 shares closed Friday at $77.23.
Berkshire once held a large stake in the Houston-based company, but shed nearly two-thirds of it in February 2014 when it swapped $1.35 billion of shares for a chemicals business that it folded into its Lubrizol unit.
Crude oil prices have since fallen by more than half, though Phillips 66's share price has dropped by less than 1 percent.
Phillips 66 spokesman Dennis Nuss on Saturday said the Houston-based company does not comment on specific shareholders.
Berkshire may have begun rebuilding its Phillips 66 stake in the second quarter, when it bought $3.09 billion of equities overall.
In an Aug. 14 SEC filing detailing its U.S. stock holdings, Berkshire did not mention Phillips 66, after having previously reported a 7.5 million-share stake as of March 31, but said it disclosed some information confidentially to the regulator.
The SEC sometimes lets Omaha, Nebraska-based Berkshire do this so Buffett can quietly buy a large amount of stock, without worrying about investors piggybacking on the famed investor's apparent stamp of approval.
He did this in 2013, when Berkshire amassed a $3.45 billion stake in Exxon Mobil Corp. Buffett sold that stake in last year's fourth quarter.
Berkshire does not normally say whether Buffett or his portfolio managers Todd Combs or Ted Weschler make specific investments, but larger investments are generally Buffett's.
Until this week, when the price briefly fell below $70, Phillips 66 shares have since April traded around or slightly above their current price.
Berkshire ended June owning $117.7 billion of equities.
It also owns more than 80 businesses, and on August 10 said it would buy Precision Castparts, which makes parts for the aerospace and energy industries, for roughly $32.3 billion.