WASHINGTON (Reuters) - The Trump administration has accepted the resignations of two top State Department officials effective on Friday, a step entirely within the new president's rights but an abrupt departure for the diplomats, officials said on Thursday.

Under Secretary for Management Patrick Kennedy and acting Under Secretary of State for Arms Control and International Security Thomas Countryman both plan to leave their posts by Friday, the officials said.

Turnover is the rule, rather than the exception, among the top officials in the U.S. government when the White House changes hands from one party to another, in this case from Democrat Barack Obama to Republican Donald Trump.

In his first week in office, Trump has illustrated stark policy differences from Obama on trade and immigration. On Monday, Trump formally withdrew the United States from the Trans-Pacific Partnership trade deal and on Wednesday he ordered construction of a wall on the border with Mexico and threatened to punish U.S. cities shielding illegal immigrants.

Political appointees chosen by the president and confirmed by the Senate were obliged, as usual, after Trump's Nov. 8 election victory, to submit letters of resignation to give the new president the opportunity to name his own people to the jobs.

Kennedy and Countryman were recently told their resignations had been accepted effective Friday, leaving their bureaus - one of which handles the department's management and the other which oversees arms control - in the hands of more junior officials.

Gregory Starr, Assistant Secretary for State for Diplomatic Security and Michele Bond, Assistant Secretary for Consular Affairs, are also leaving, officials said, though it was not clear under what circumstances or whether they were asked to step down by Friday.

Trump's nominee for Secretary of State, former Exxon Mobil Corp chairman Rex Tillerson, has yet to be confirmed by the full Senate, leaving the agency in the hands of number three official Under Secretary of State for Political Affairs Thomas Shannon.

The departures were discussed at State Department Thursday morning meetings and caused some unease, in part because at least two of the officials had been asked to go by Friday.

"It's not two weeks' notice," said one official who spoke on condition of anonymity.

However, the department itself stressed that turnover is the norm when a new political party comes to power.

"Of the officers whose resignations were accepted, some will continue in the Foreign Service in other positions and others will retire by choice or because they have exceeded the time limits of their grade in service," acting State Department spokesman Mark Toner said in a statement.

It did not provide a detailed breakdown of whose resignations were accepted or when they were leaving.

At least one media report suggested that the departures amounted to a mass resignation, but several U.S. officials said this was not the case.

"It's not a mass protest or a show of indignation," said one senior U.S. official.

A former senior Obama administration official said there were no plans at the National Security Council for a mass resignation and that recent conversations there with Trump’s inner circle had been viewed as productive and encouraging.

The State Department departures amounted to a "huge brain drain," the former official said, adding that their collective experience would be difficult to recover.

However, a current State Department official rejected this view, saying that while Kennedy, in particular, was seen as an institution, he could certainly be replaced.

"Everybody is (acting) like it is a big apocalypse. He has large shoes to fill, but the culture of the State Department is about change and moving around every few years," said the official. "It’s not like the building is going to fall apart."

(Reporting by Lesley Wroughton, Arshad Mohammed, Jonathan Landay and Dustin Voltz; Editing by Yara Bayoumy and Grant McCool)