It would help if you explained your data a little more; how is it set up?
For example, if you actual time is like at = [1,2,4,5] for a 5 minute interval, you could do something like this:
observed_times = [1,2,4,5];
observed_data = [14.1,12.2,3.4,1.1];
t = [1:5];
[~,ind] = ismember(t,observed_times);
impute_data = [NaN,observed_data];
ind = ind + 1;
corr_data = impute_data(ind);
Your new time series would be t,|corr_data|. I used NaN here instead of a zero because you might actually have zeroes here, but you can easily change this.
