But the former party chairman did not deny that the bombshell sex attack claims about an unnamed member were true.
Mr Dowden told the BBC it was “very difficult for me to comment” without knowing the suspect’s name and with a possible police inquiry ongoing.
He spoke after another ex-party chairman Sir Jake Berry was said to have written to police about the colleague at the centre of the claims.
Mr Berry, together with Chief Whip Wendy Morton, told officers only limited action had been taken against the alleged attacker.
He said he became aware of the scandal because the party had paid for one of the victims to have treatment at a private hospital.
His colleagues’ failure to take action was feared to have left the MP free to attack up to five separate women.
The scandal was revealed in a serialisation of former Culture Secretary Nadine Dorries’ new book The Plot: The Political Assassination Of Boris Johnson.
Other claims include one that an MP had sex with a prostitute on a billiard table while four other members watched cheering.
Another MP was said to have stored a laptop containing indecent pictures of children for a relative and another videoed while having adulterous sex.
Mr Dowden told Sunday With Laura Kuenssberg: “These are very serious allegations and I want to reassure that the Conservative Party takes them exceptionally seriously.
“It is very difficult for me to comment specifically on this for two reasons. First of all, the individual isn’t name and secondly, it may be the case that there are criminal investigations ongoing.
“But what I can say is that every single allegation is taken exceptionally seriously.
“We had an independent investigation process into it and indeed if anyone has concerns, they should be taken to the police and I would urge people to take them to the police.”
Sir Jake, who was chairman for a month under Liz Truss’s brief Premiership, found the hospital bill for the alleged victim’s treatment.
It is not clear which police force was contacted but he told them they were concerned about the “scant information” given about how the MP – referred to as “X” – was dealt with.
“Additionally, neither were we satisfied that enough effort had been made to ascertain the nature of the allegations against X.
“Nor were we sure that victims had been properly advised about relevant procedures to bring a complaint.”
They went on to order a Downing Street adviser and a senior MP to launch an internal investigation into the allegations.
Their report said: “It is my view that if this did end up in court, not only would [one of the alleged victims] be poorly served and have a poor success rate but the party would be severely at risk of prosecution because of the peacemeal [sic] approach we have applied in this case and no doubt others.”
The report revealed there had been two known rape complaints against the same MP.
One was the vulnerable woman who required hospital treatment after her mental health deteriorated following the attack.
A second victim claimed she was “date-raped” at the Conservative Party conference, did not want to complain to police but suffered a “spree” of discrediting from her attacker.
The Tory report added: “It highlights the serious lack of process within the party to protect both the victim and the people being accused.
“We still have a ‘innocent until proven guilty’ legal system in this country and the way this had been handled, protects neither the victim nor X who has been accused of very serious offences.”
