Henderson, who is back in Dunedin as he considers the next move in his career, said the whole issue involving Froome came back to therapeutic use exemptions.
Froome was cleared last week to ride in the Tour de France and was 1min 7sec off the lead yesterday after the first two stages.
Froome was under investigation for an adverse analytical finding for elevated levels of asthma drug salbutamol at last year's Vuelta a Espana.
The case, which was meant to remain confidential, leaked into the public domain last December, but the UCI did not initially ban the rider.
He was cleared by the UCI last week when the it released a statement admitting it had received information from the World Anti-Doping Agency that made it abundantly clear that the UCI's disciplinary body would be unable to prosecute Froome.
Froome is a four-time winner of the Tour de France and is heavy favourite to win again this year. Froome has been given a TUE as he suffers from asthma.
Henderson, who retired from competitive cycling last year and is now concentrating on coaching, said he was not the only one who was at a loss how Froome could be competing on the tour.
``I do not understand how that is possible, how he can compete. That is what everyone can't understand. How it is possible for a guy who has tested positive but has now survived and has now raced?'' he said.
``There are boys out there who have had less in their system and been banned. If I was one of those guys I would be spitting about it.''
Henderson said he could understand the higher level of the salbutamol found in Froome's system if it was out of competition.
Maybe if it was pre-season and he suffered an injury and took medication to get back to full fitness while building for the season, it could be considered, Henderson said.
But Froome's high levels were found while he was competing in one of the grand tours.
``The levels found is his system were ridiculous.''
Henderson said he would hate to think how the Tour de France and cycling in general would cope if one of the top riders in the tour this year was caught cheating with drugs.
Henderson had competed in the Tour de France mainly for the Lotto-Soudal team and had also ridden for Team Sky, which is Froome's team, in 2010-11.
Team Sky finished outside the top 10 in the years Henderson cycled for it but in 2012 Bradley Wiggins won the Tour and Froome finished second. Team Sky has been top of the tree since.
``They found out what worked for them and did not work for them.''
