UPDATE: Boom will start THE first stage despite showing low levels of cortisol in a test on the eve of the race.
"Boom will take the start," Astana team boss Alexander Vinokourov said.
The decision means Astana will in all liklihood recind its membership in the organisation.
Low levels of the hormone can be explained by the use of corticoids, anti-inflammatory drugs that are allowed out of competition but forbidden while racing unless a rider is granted a Therapeutic Use Exemption (TUE).
Astana, the team of defending Tour champion Vincenzo Nibali, are members of the MPCC (Movement for Credible Cycling) that applies stricter rules than the International Cycling Union (UCI) and the World Anti-Doping Agency (WADA).
"According to article 9 of the MPCC the return to competition will be made after at least eight days of rest," the MPCC said in a statement on Friday.
UCI regulations do not forbid Boom from starting Saturday's first stage, a 13.8-km individual time trial.
Team manager Alexandre Vinokourov suggested Astana could leave the MPCC so that Boom may begin the race.
"Either the UCI allows us to replace Boom or he starts with us. Never mind the MPCC," the Kazakh told the French sports daily L'Equipe.
Astana said in a statement that they had asked the UCI if Italian reserve Alessandro Vanotti could take the Dutchman's spot in the squad.
"Official registration of riders for the 2015 Tour de France closed at 1030 on 3 July at the sport directors' meeting (before the team were notified)," Astana said.
"Alessandro Vanotti will arrive in the Netherlands Saturday morning to undergo physical and blood tests and await a UCI decision on the matter."
Astana were last year faced with being stripped of their World Tour licence following positive dope tests and only learned they had retained their elite status in late April.
"Our team is followed closely. Our training programme has been spoken about and we've paid the price for the riders who doped but we can't pay the price for mistakes we haven't made ourselves," Nibali said earlier on Friday.
At 14:00 on 3 July, Astana Pro Team received analyses from the UCI's independent antidoping agency CADF from blood tests administered to its nine Tour de France riders on 2 July -
According to the CADF notification, rider Lars Boom has a healthy and permissable level of cortisol for the Tour de France that is however too low for applicable standards from the MPCC.
In response to official correspondence from the MPCC from 29 June 2015, Astana Pro Team asked the UCI to authorize the activation of named reserve rider Alessandro Vanotti to the Tour de France squad in order to start on 4 July.
Official registration of riders for the 2015 Tour de France closed at 10:30 on 3 July at the Sport Directors' Meeting, before the CADF notification.
Alessandro Vanotti will arrive in the Netherlands Saturday morning to undergo physical and blood tests and await a UCI decision on the matter.