He stated this at a news conference on Saturday in Abuja.
He, however, noted that there had been some isolated incidents of security checks reportedly carried out on some newspaper delivery vans in the last few days.
The presidential aide added that the media as the fourth estate of the realm, was held in very high regards by the President.
This, he said, had been practically demonstrated in various ways by the President Goodluck Jonathan-led administration in the last three years.
He recalled that it was President Jonathan who signed the very contentious Freedom of Information Bill into law on assumption of office.
Okupe noted that the President had consistently espoused the principles of openness, accountability and liberalism in his relationship with the media at all times.
"The reported incidences of checks being carried out by the military on major Nigerian roads and cities is not targeted at newspaper vans because of the contents of the publications as insinuated.
"Rather, the military had explained that those routine checks were being carried out following intelligence reports," he said
He stressed that there had been reports that of some elements within the society planned to use such vehicles to convey materials with grave security implications across the country.
"While we sympathise with media houses which might have suffered one discomfort or the other as a result of these security checks we assert, for the avoidance of doubt that the President has not and will never give any order capable of hampering the smooth running of any media organisation," Okupe stated.
He added that government would neither engage in nor encourage any acts that would constitute an assault on any media organisation or infringe on the freedom of the press.
According to him, the military has assured that no personal liberties of media practitioners or their employees will be unlawfully tampered with.
He added that as soon as there was significant reduction in the level of the security alert, the ongoing exercise would be relaxed.
The presidential aide further maintained, that because we live in very trying times, some sections or sectors of the society might experience some temporary discomfort.
This, he said, was in the overall interest of ensuring that the ideals of freedom, peace and security is not compromised by a few unscrupulous elements in our midst.