Speaking in his weekly televised address on Friday night, the coup leader also defended the new interim constitution, and repeated his call on the media to present news and information accurately and with honest intent.
The National Council for Peace and Order (NCPO) has spent the past week defending a new media policy that journalists say amounts to intimidation and makes it difficult to do their jobs.
"I want to thank leaders of all political groups for not starting political movements but engaging in personal activities, take a rest, exercise, being with their families and preparing for national reform," Gen Prayuth said.
"We hope we will receive more cooperation from all sides to bring about national reconciliation and reform and to overcome the fog that has long been obstructing the country from moving forward."
Discussing the provisional constitution, Gen Prayuth said it sought to maintain a balance between the powers of the interim government and those of the NCPO. Critics say the document gives the NCPO an iron grip over every aspect of national administration.
"The NCPO has no desire for power or personal interest," the junta leader said.
Gen Prayuth also defended the NCPO's decision to freeze local elections, saying the ban affected only a few hundred out of several thousand local administrations.
There were fears in some quarters that the NCPO would stunt democratisation in the provinces by curbing the elections of tambon and provincial administrations after the military ordered a freeze on local elections. Gen Prayuth reassured that this was not the case, noting that the NCPO had allowed the Election Commission to endorse the results of elections that took place before the May 22 coup.
In the past, the selection method was not transparent in some areas while some of the people holding office were not effective.
"The NCPO doesn't see serious problems here. Some reforms might be needed for more transparency and fairness. We have never intended to make drastic changes in local administrations," he said.
He also urged the media to correctly understand the NCPO's intentions.
He said the council was not obstructing the media but wanted to create fairness.
Media representatives take a different view, saying that new provisions barring criticism of the NCPO or its staff are very broad and would make it difficult for journalists to carry out their duties.
"We're not trying to take control of the media but we want all types of media and media associations to be strong and credible in the people's eyes," said Gen Prayuth.
"I ask the media, the Thai Broadcast Journalists Association and foreign journalists to understand the work of the NCPO as it has to create as much peace and order as possible in the country now."
Problems would only arise for media representatives, he said. "if you over-criticise or don't have an honest intent".
He said the NCPO needed cooperation from the media because they had the power to create peace or unrest.
"In the second phase, there will be reform in all branches of the media and all media members must help and cooperate," he added.
Discussing the provisional constitution, the army chief said it sought to maintain a balance between the powers of the interim government and those of the NCPO.
He said it was necessary for the document to clearly define the scope of authority and duty of organisations established under it, stressing that these organisations exercise powers on behalf of His Majesty the King.
The interim charter is now in effect following the declaration of its promulgation in the Royal Gazette on Tuesday.
"Everyone should be happy that there is a balance of power between the government and the NCPO," he said.
He was responding to criticism that Section 44 of the interim charter gives the NCPO power over the interim government, which is to be formed soon.
Section 44 authorises the NCPO leader to exercise the powers of the executive, legislative and judicial branches to promote reform and unity, and to prevent and suppress threats to national security, the royal institution, and the economy. The actions and orders of the NCPO leader are deemed legal and constitutional.
Gen Prayuth told his audience on Friday that those who would be given powers under the interim charter should not worry about the scope of the NCPO's power, as long as they exercise their own authority in the best interests of the public and the country.
He also criticised the people who claimed to be "calling for democracy" in the country.
He said civil servants were unable to truly work for the general public in the past because of corruption, collusion and the lack of transparency in the system.
He said he did not understand how people who claimed to be pro-democracy activists could overlook the difficulties authorities had been facing, particularly protecting and securing people's lives and property. There had been protests in 2006, 2010, 2013 and 2014 and each side claimed that it was fighting for democracy.
"The NCPO must end this conflict and solve the problem in a sustainable manner. If they can see this they'll understand us. If you condemn us as we're trying to fix the problem, this won't be right and we ask for fair treatment," said Gen Prayuth.