Unfortunately, space-delimited files aren't very amenable to such shenanigans; one way would be to read the file on a line-by-line basis and determine there whether there is a missing field or not and skip it if so.
Alternatively, you can read into a cell array and work on it -- Matlab can't handle "jagged arrays" as ordinary arrays so the cell or a structure or the like is the alternative.
Probably the best way would be to have the application that creates the file tag the missing values w/ an indicator value for missing -- 'NaN' or some other indentifiable value. Or add a specific delimiter that can be read to indicate the missing field.
