The MEA, however, cleared Reddy's visit to the United Kingdom.
The clarification came after the Telangana Chief Minister's Office announced that Reddy had cancelled the US leg of his foreign tour after the Centre declined permission.
MEA explains decision
MEA spokesperson Randhir Jaiswal said on Friday that visits by chief ministers and other dignitaries are assessed before political clearance is granted.
"The programme proposed in such cases should be appropriate to the office held and the purpose of the visit," Jaiswal told reporters.
"In this particular case, that was not so with respect to the United States. Therefore, the clearance was denied and not given," he said, while confirming that clearance had been granted for Reddy's UK visit.
Telangana government calls decision 'political'
Reddy's office said the Telangana government had followed the required procedures and sought permission from the Centre for his proposed visits to both the UK and the US.
According to the Chief Minister's Office, permission was initially granted only for the UK leg. After the official delegation had already reached the UK, the state government was informed that clearance for the US visit would not be granted.
The CMO alleged that the decision was taken on "political grounds".
"Nevertheless, respecting the Centre's decision, he decided to return to Hyderabad from London instead of proceeding to Boston, USA," the statement said.
What was on Reddy's US itinerary?
Reddy had been scheduled to visit the US after completing his UK engagements.
His itinerary included visits to the campuses of Harvard University and MIT on August 24. On August 25, he was scheduled to visit the North-Eastern campus and meet a team from Virginia Tech University in Boston.
A 'Meet and Greet' event organised by the Indian Overseas Congress (USA) was also planned in New York on August 26.
Reddy was scheduled to return to Hyderabad on August 30 but will now return from London instead.
UK visit gets Centre's clearance
While the Centre blocked the US leg of the trip, the MEA confirmed that political clearance had been granted for Reddy's visit to the UK.
The differing decisions over the two legs of the tour have triggered a political dispute, with the Telangana government questioning the Centre's reasons for denying permission to the US visit.