No. Intonation is a different thing. It usually happens when you put new strings.
I don't know the proper technicalities of this, but I will explain it the way I see it.
Intonation means accuracy of pitch. The ability of your instrument to reproduce the correct pitch corresponding to the note that you play. That means, that when you play the 0th and 12th frets on the high E string, the notes would always be an E. That also means that the harmonics are correct as well (that is how I check the intonation of the guitar).
When the intonation goes off, that means that the guitar is not producing notes accurately. That is, when I play an open E on the high E string on a properly tuned guitar, the note will be an E, but if I play any consequent notes, they might either be slightly sharper of flat. That means, the higher up the fretboard you play, the more inaccurate your notes become and anything you play will sound like crap, regardless of how well you tuned your guitar. That means, if the note at 0 is an E, the note at 12 could be slightly sharper or flatter than E or in the worst case, F or D#.
This problem can usually be fixed by modifying the string length via the bridge saddles. If the notes are sharper, the string length is increased and if the notes are flatter, the string length is increased. But certain factors require you to go to the repairman.