Ligomeka has described the ban as a huge blow to media freedom, diversity and development in Malawi.
He has also called all media organisations to engage the government in dialogue in resolving the issue instead of rushing making condemnations.
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"I have indeed heard rumours, or should I call them reports that government is not advertising in The Nation Newspaper. I have not seen authentic documentation on the same but I hear that there are some circulars flying in some parastatals about the alleged ban.
"If it is indeed true, the development is a huge blow to media freedom, diversity and development. It has actually come at a wrong time in the sense that I thought government would take advantage of Nation's vernacular publication Fuko to place advertisements targeted at the rural masses," Ligomeka told Tribune.
He said he would not rush to condemn government as that is not the best strategy in his view.
"If we rush to condemn government in a statement, what will we achieve? There are times for condemnations and times for other strategies to deal with this serious crisis. MISA will come up with a position after its National Governing Council meets.... and we are meeting soon.
"My personal position, however, on this on this matter is to engage authorities so that we find the reason why the government has meted out this ban. Authorities should be engaged in dialogue and find an amicable solution," he said.
Ligomeka added: "We need government officials, Media Council of Malawi, Journalists Uaidnion of Malawi, Malawi Human Rights Commission and the leadership of The Nation and other influential bodies to resolve this matter through dialogue and contact. I don't think a mere, hurried condemnation is the first best option. If we condemn government today, can we turn around tomorrow and call for negotiations with them to lift the ban?"
Ligomeka implored government to seriously consider rescinding its decision because advertising is the life blood of every vibrant private media institution.
"Much as government has its preferences when it comes to choosing which media organisations to advertise with, but the directive to stop advertising with The Nation Newspapers in MISA's view has negative consequences on media development.
"I appeal to government to take our appeal and welcome us as we will be discussing this issue with its officials in trying to reach an amicable solution. We need to discuss this soberly because we don't want others, foreign organisations in particular, to start condemning government that it is suffocating the media," he said.
He said with the Constitution guaranteeing media freedom government has an obligation to safeguard press freedoms instead of suffocating the media organisations.
"President Bingu wa Mutharika is a good friend of the media, I hope when he hears about this problem he will come to our rescue. I like him because when the media requests him for meetings, he happily accepts that. He also holds regular press conference with members of the media. I don't think this ban has his blessing. Let's keep our fiungers crossed as we will be going into discussions with those in government," he said.