"On 17th February, I will step down as the president, but I will carry on my duties as an ordinary citizen in connection with doping," Balakhnichev told Reuters.
"We have submitted two cases to a Russian court in order to defend the honour and integrity of the VFLA. We will pursue (programme-maker) Hajo Seppelt and those people who were hired for him in order that he could complete his scandalous task.
"We are also preparing a case in a German court against the ARD company and against Seppelt himself. We have a strong case," Balakhnichev said.
The three-part documentary, broadcast by ZDF/ARD in December, featured an undercover video of what it said were Russian athletes and coaches admitting to covering up positive drugs tests.
The allegations have not been verified by Reuters and Balakhnichev denounced them as "a pack of lies".
Russian anti-doping agency RUSADA suspended a number of Russian athletes in January, including Olympic walking champions Olga Kaniskina, Valery Borchin and Sergei Kirdyapkin.
Yulia Zaripova, who won gold in the women's 3,000 metres steeplechase at the 2012 London Olympics, was also banned.
"I stated earlier that this would be my final four-year stint as the President of the VFLA, so I would have stepped down in 2016. However, the recent events have sped up this process," Balakhnichev said.
"As I am responsible for the VFLA, including anti-doping measures, I believe my position is untenable. I took it upon myself to take responsibility for everything that has happened and on 17th February at a VFLA session meeting, I will step down."
The first vice-president of the VFLA, Vadim Zelichenok, will take temporary charge of the organisation.
"He is an experienced specialist. He will be the president until 2016. Who will replace him? This is not a question for me. The 75 regions of Russia will make this decision," Balakhnichev said.
(Editing by Ed Osmond)
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