Hey OnlineGame,
''By no means'' is an idiom that means the same as ''definitely/absolutely not'' ; ''not at all''. Such meaning is the opposite to that of ''by all means''. So far as that is concerned, the usage of ''by no means'' in the example you provided conveys the idea that ''It is definitely not certain that we will finish this project by June!'' or even ''We definitely won't finish this project by June!''.
Here is a set of examples that may help you understand it better:
E.g.: ''By no means shall our country be drawn into yet another war overseas.''
E.g.: ''I am by no means a friend of his.''
E.g.: ''He is by no means a weak opponent.''
E.g.: ''He has not won yet, not by any manner of means.''
The usage of either ''by no (manner of) means'' or ''not by any (manner of) means'' is also permissible should you want to emphasize a fact or situation.
Hope that helps!!! :)