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It depends that how less the marks really are!
You can still find out colleges that do not require high percentage as eligibility criteria for taking admission in M.Sc maths. Scoring less is not an issue, a number of colleges provide admission even though a candidate has less marks in previous qualified degrees. You find out more about such institutes which invite applications for your desired course. Go to their website, if the college is in your hometown, visit the same. Or else call on the toll free numbers of various Universities and enquire about the eligibility criteria as well as admission procedure.
I am sure, you would find one. However, yes, work hard this time and fetch good marks in M.Sc. As you know, the graph should go upward as you proceed further with your career, as this will justify your performance and seriousness as a candidate for job or so.