RUSADA executive director Nikita Kamayev said the World Anti-Doping Agency (WADA) was conducting an investigation after one of Pishchalnikova's samples tested positive for an anabolic steroid.
"WADA asked RUSADA to take a sample from Pishchalnikova. The test found the presence of a heavy substance (anabolic steroid)," Kamayev was quoted as saying by local media.
"The test came out positive - it's a fact and now we must wait for the official statement."
Pishchalnikova, who won the 2011 discus world title in Daegu, South Korea, and finished second at the London Olympics this year, proclaimed her innocence and requested analysis of the B sample.
She has already served a doping ban of two years nine months from July 2008 to April 2011. The 27-year-old was among seven leading female Russian athletes found guilty of manipulating drug samples before the 2008 Beijing Olympics.
She also won silver at the 2009 world championships in Osaka, Japan, but was stripped of the medal after the sport's governing body the IAAF annulled all her results from May 2007.
"In practice, an athlete who commits a second offence involving (anabolic steroids) could face from eight years to a life ban," said Kamayev.
"As for the Olympic silver medal, it depends when her suspension would start if she was found guilty this time."
Valentin Balakhnichev, president of the Russian athletics federation (VFLA), said Pishchalnikova's case should be finished by the end of the month.
"I can't make a full disclosure of her case because the due process has not finished," Balakhnichev told Reuters.
"The athlete has a right for the B sample to be tested so it will take some time. But we should make a decision on her case within the next two weeks unless she files an appeal," he said.
"I'd like to make it clear that (VFLA) is committed in the fight against doping. Unfortunately, this is not an isolated case. We have seen quite enough such cases in Russian sports. Still, this is shocking news to me."
The VFLA on Wednesday banned former European 10,000 metres champion Inga Abitova for an "abnormal haemoglobin profile in her biological passport".