My paper was accepted by a publisher; an acceptance letter was mailed to me. However, later my institution didn’t allow me to publish there, because it the journal isn’t indexed by Scopus? How can I withdraw the paper; is there any issue if I submit my paper to another publisher?
Your question is the result of going against the grain. You should have looked first if your university had any rule regarding which journal to publish. This is important even now as you can re-submit to another unwanted journal by the university.
Depending on the limited data given by yourself I suggest you get a confirmation from the journal that your article will not be published by them. Until that time, do not send your article to another journal for review. . Again I assume that perhaps you wanted to fund the article through university and that is why university refuses article. Is this the case? If it is, then you should either publish without any funding from the university or follow above mentioned suggestion.