"I am bitterly disappointed that data extraction from the former Moscow Laboratory has not been completed by the date agreed," said WADA president Craig Reedie.
WADA said the independent Compliance Review Committee (CRC) will now consider the next step in the long-running saga at a January 14-15 meeting.
The end-of-year deadline was set in September, when WADA lifted a ban on the Russian Anti-Doping Agency (RUSADA), paving the way for Russian athletes to return to competition across all sports after a report which uncovered a state-sponsored doping programme in Russia.
WADA's confirmation of the missed deadline came as US Anti-Doping Agency chief Travis Tygart described Russia's return to the sports fold "a total joke and an embarrassment".
However, in his New Year message, International Olympic Committee president Thomas Bach insisted sporting superpower Russia had been sufficiently punished.
"With its suspension from the Olympic Winter Games PyeongChang 2018, the Russian Olympic Committee has served its sanction," wrote Bach.
WADA personnel travelled to Russia in December but were unable to extract all of the promised data.
WADA said at the time its team could not complete its mission "due to an issue raised by the Russian authorities that the team's equipment to be used for the data extraction was required to be certified under Russian law".
With WADA waiting and the December 31 deadline looming, RUSADA chief Yury Ganus asked Russian President Vladimir Putin to intervene to stave off another ban that put Russia "on the brink of the abyss".
However, the Kremlin said RUSADA's concerns about new sanctions were "without foundation."
Reedie added on Tuesday: "WADA has been working diligently with the Russian authorities to meet the deadline, which was clearly in the best interest of clean sport. The process agreed by WADA's ExCo in September will now be initiated."
That process will now see the independent Compliance Review Committee meet on January 14 and 15 to examine the developments before a recommendation is made to WADA.
That could lead to RUSADA again being declared non-compliant.
Tygart said Russia missing the deadline should come as no surprise.
"In September, WADA secretly moved the goal posts and reinstated Russia against the wishes of athletes, governments and the public," Tygart said. "In doing this WADA guaranteed Russia would turn over the evidence of its state-supported doping scheme by today.
"No one is surprised this deadline was ignored and it's time for WADA to stop being played by the Russians and immediately declare them non-compliant for failing yet again to meet the deadline."
Last month, the governing body of world athletics (IAAF) said they were maintaining Russia's ban from track and field over the state-backed doping controversy.
Russia's athletics team was barred from the 2016 Rio Olympics and also missed the IAAF World Championships in London a year later.
A number of Russian athletes, however, have been granted permission by the IAAF to compete as neutrals after meeting the exceptional eligibility criteria, essentially demonstrating that they have come through transparent anti-doping testing.
The IOC lifted its ban on Russia at the end of the Pyeongchang Winter Olympics.
Later Tuesday, the athletes commission of the UK Anti-Doping Agency called for Russia to be declared non-compliant.
"The Russian state need to prove unequivocally that they have learned from the biggest doping scandal under WADA's watch," said a statement.
"And that they will be committed to a drug-free, transparent regime across international sport.
"Otherwise WADA..must now declare RUSADA non-compliant."AFP