A press release stating that the Presidency had put a "blanket ban" on marches to the Union Buildings in Pretoria was false, the ministry said on Tuesday.
It was responding to an organisation called Equal Education (EE) saying that it had been banned from marching to the buildings on March 26.
"The Presidency wishes to place on record that it has not instituted any ban on marches to the Union Buildings," it said in a statement.
"The Presidency upholds the right of all citizens to freedom of expression and peaceful demonstration."
The ministry would continue to work with all relevant parties to ensure that such rights were exercised within the law.
The organisation said earlier on Tuesday that it would launch an urgent legal application to "overturn the prohibition of a march". It said notice was given to Tshwane metro police department (TMPD) more than a month in advance and since then the metro had repeatedly refused EE the right to march to the Union Buildings.
"The reason TMPD gives is a blanket ban on all marches to the Union Buildings as directed by the DG in the Presidency, Mr Vusi Mavimbela. We have given extensions and now resort to legal action as a last resort."
The Presidency said following last year's illegal march by soldiers to the Union Buildings, which ended in violence, it had sought to improve the management of marches to its premises. This was by working with the Tshwane metro and the relevant departments.
"The Presidency always encourages march organisers to channel whatever issues they may have to the relevant departments. We would encourage people only to march to the Union Buildings as a last resort."
The ministry said that it was ready to talk to the parties involved to ensure an amicable outcome.
EE said that the purpose of the intended march, largely by EE members, school children and parents, was to highlight the need for access to books and libraries.
Marches were also planned during South African Libraries week at the end of March in Cape Town and Polokwane.
The Tshwane community safety department also rejected the "so-called" ban as false.
"As clarified by the Presidency... there is no blanket ban on marches to the Union Buildings. Nor is there a ban on marches in the city," spokesperson Console Tleane said.
The "confusion" emanated from correspondence received from the Presidency in November 2009.
This advised that all marches to the Union Buildings would be suspended, but not banned, until further notice.
"This was a reasonable request emanating from the violent march by the soldiers to the Union Buildings. Everyone was agreed at the time that the incident was undesirable."
Tleane said that EE's application was received in February, but was turned down because the Presidency had requested marches to the Union Buildings be suspended.
"The Tshwane metro police respects and upholds the right of citizens to express themselves." Being the metro in the capital city it was inundated with applications for marches.
"We process an average of ten applications per week. Our record speaks for itself, that we assist applicants accordingly."
He said that the metro would not oppose the court application and would fulfil its mandate to process applications within the two-week designated period.
"In the light of the latest letter to Equal Education by the Presidency and the statement released by that office, we are approaching them (the Presidency) so that we can smooth this matter and ensure that citizens enjoy the right to express themselves," Tleane said.