One approach, taking advantage of the fact that both of your matrices are sorted by the first column:
M1 = sortrows(rand(15, 4), 1);
M2 = [M1(1:5:end,:) rand(3,2)];
idx = find(ismember(M1(:,1), M2(:,1)));
M1 = [M1 zeros(size(M1,1),2)];
M1(idx,5:6) = M2(:,5:6);
Since you are dealing with floating-point numbers, if you have R2015a or later, you would likely best use ismembertol instead of ismember to guarantee that your data match.