A washout after each injections (or perhaps after every "n" injections) should work, but has drawbacks, as has been pointed out.
The other approach is to get rid of the contaminants before they get to the column. That requires that you figure out if they are coming from the sample or the mobile phase. That requires investment of a day or so: run a series of samples, wait for a long while (with the pump running), then run another series of samples. Plot retention versus sample number and then plot retention versus total elapsed time. 
If the contamination is coming from the mobile phase, the 'versus sample number" plot should have a jump in the middle (corresponding to the waiting period), while the 'versus time" plot should be more linear. 
If the contamination is coming from the sample, the "versus sample number' plot should be reasonably linear, while the 'versus time' plot should have a plateau corresponding to the waiting period.
We have this slightly better documented in the 
LC Troubleshooting Wizard on our web site:
http://www.lcresources.com/resources/TSWiz/hs390.htm