Yes. As of March 2012, "The Ambassadors of Death" and "The Mind of Evil" are only available on black and white or mixed black and white/colour videotape. The former story has been fully colourised and is due for release soon; the latter hasn't been started yet. Everything else is available in colour.
They were all filmed originally in colour, but many were lost, because of the BBC policy of wiping videotapes.
Fortunately, for all of the Pertwee stories (unlike the first two Doctors), there were copies in oher countries (or even other divisions of the BBC).
Unfortunately, most broadcasters in other countries didn't transmit colour yet, so those copies are in black and white. The US did transmit colour, and copies of all but two stories were found there, but the US uses a different standard from the UK (NTSC instead of PAL), which means the videos had been converted, and would then have to converted back if the BBC wanted to use them, and the quality would be far too low to be worth it.
Fortunately, the Doctor Who Restoration Team has come up with some pretty nifty tricks that allow them to re-create the original colour footage from a high-quality black and white and a low-quality colour source. See the link below for more information on how this works. Over the past few years, as they complete each story, it's released on DVD. For "The Ambassadors of Death", the only complete NTSC colour copy was heavily degraded, with frequent dropouts, which made it much harder. For "The Mind of Evil", there is no complete colour copy. That's why these two were saved for last.