Washington announced the plans in June, portraying such contacts as the continuation of an earlier policy. But analysts said it reflected a new approach to the way it dealt with a group which Mubarak banned from politics.
The Brotherhood is one of Egypt's most popular and organised groups, with a broad grassroots network built up partly through social work even in Mubarak's era.
The contacts may unsettle Israel and its U.S. backers. The Brotherhood renounced violence as a means to achieve political change in Egypt years ago. But groups like Hamas, which have not disavowed violence, look to the Brotherhood as a spiritual guide.
Under the previous policy, U.S. diplomats were allowed to deal with the Brotherhood's members of parliament who had won seats as "independents" to skirt the official ban. This provided a diplomatic cover to keep lines of communication open.
"We have had direct contacts with senior officials of the Freedom and Justice party," the senior diplomat told Reuters, referring to the Brotherhood's party that was founded after politics opened up following the ouster of Mubarak.
The diplomat said U.S. officials did not make a distinction between members of the Brotherhood or its party. "We don't have a policy that makes a distinction, that one or the other is off limits," he said, without saying when the meetings took place.
The diplomat was responding to a question about whether any meetings had occurred, after Freedom Justice Party Chairman Mohamed Mursi told Egypt's Al-Dostour newspaper last week that U.S. officials had not made contact since the policy shift.
Speaking to Reuters on Sunday, the party deputy head Essam el-Erian also denied any meetings had taken place with U.S. officials when asked about the diplomat's comments.
It was not immediately clear why the two sides gave different accounts.
'HIGH-LEVEL' MEETINGS
Under the former Egyptian president, the Brotherhood was banned and its members often detained. Mubarak often presented himself as the bulwark preventing Egypt's slide into Islamist hands, an approach that analysts said help secure him backing from Washington and other Western powers wary that Egypt could turn into another Iran or Gaza.
The group took a backseat in the early part of the anti-Mubarak uprising, which was broadly led by youth groups who put national concerns above religion. But the Brotherhood and its party have taken a increasingly prominent role since.
The diplomat said the U.S. contacts had been with "high-level" members of the Brotherhood's party but did not give names. From the U.S. side, he said the contacts were not at ambassadorial level but he did not give further details.
"We had occasionally had these contacts in the past ... The difference is in the past we had seen parliamentarians," he said.
Egypt's parliament was dissolved after Mubarak's fall. Fresh elections for the lower house are due to start in November, with a vote for the upper house early next year.
The Brotherhood is expected to perform well in the vote, although many analysts expect a fairly fragmented parliament with no single unified voice emerging.
The diplomat said contacts with the Brotherhood were part of an effort to understand Egypt better and explain U.S. policies.
"From our perspective it is important to be in touch with all of the emerging political forces here in Egypt, across the board, that are peaceful and committed to non-violence," he said.
"It helps to understand Egypt and the way the political system is developing, and it helps us to deliver our message and get them to understand where we are coming from," he added.
(Additional reporting by Tamim Elyan; Editing by Rosalind Russell)
