In a statement the Football Conference said: "Whilst acknowledging some creditors have been paid, the club has been unable to evidence it has fully achieved this requirement."
Jon WilkinsonBBC Northampton Sport
Both the points deduction - and the player registration embargo remaining in place - are blows to the Poppies' hopes of Conference survival.
But the HMRC winding-up petition hearing on 2 April is more threatening to the club's existence.
They are only three points from safety but fans remain uncertain where the club is heading despite great efforts from volunteers and 'club men' like Ken Samuel.
Kettering have the right to appeal against the decision.
George Rolls, who is in discussions over a potential takeover at Nene Park, said on Thursday
some creditors had received their money
while proposals were in place to settle any other outstanding payments.
But, after failing to satisfy the Football Conference that they have a repayment structure in place, the relegation-threatened Poppies will fall three points adrift of Blue Square Bet Premier safety.
In a statement Kettering said: "Those currently running the club are naturally disappointed that, despite being able to pay a number of outstanding football creditors, and coming to agreement with the remaining fit players at the club, there still remained some claims from football creditors (some disputed) which were unable to be dealt with within the time span.
"The situation was further exacerbated by claims to the Football Conference from former employees which were not made clear to us within the time frame."
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.