Kovalainen was due to be present for the curtain-raiser at Fuji Speedway on July 18-19 to drive for the SARD Toyota team alongside regular co-driver Yuichi Nakayama.
However, the Finn was one of several drivers forced to skip the pre-season test at the same track last weekend because of the rules that prevent travellers from 129 countries from being able to enter Japan, put in place because of the global coronavirus pandemic.
Now Kovalainen has confirmed that time has run out for him to be able to be present for the Fuji opener, with little prospect of the entry restrictions being lifted in the near future.
"I'll miss the first race, I won't be able to enter Japan," the one-time grand prix winner, who is currently in his native Finland, told Motorsport.com. "We were hoping the restrictions would be eased in July but it hasn't been the case, so I have no choice but to miss the race.
"I really don't know when I'll be able to enter Japan; we thought July would have been OK but it wasn't the case, so I'm not sure if August is going to be any better. I'm ready to go anytime and flights are available easily, so I can go whenever the restrictions open.
"Once I can travel to Japan, I will most likely stay there the rest of the year to make sure I'm around when our season is running."
#17 KEIHIN NSX-GT
The absence of Kovalainen and Baguette will leave only four non-Japanese drivers in the GT500 division for the Fuji race: Nick Cassidy, Sacha Fenestraz (both TOM'S Toyota), Ronnie Quintarelli (NISMO Nissan) and Jann Mardenborough (Kondo Nissan). It marks the smallest number of foreign drivers in SUPER GT/JGTC's top class since 2000.
A spokesperson for series organiser GTA said that it "continues to make requests to the ministry in charge of the matter" when asked for an update by Motorsport.com on its efforts to secure an exemption to the entry rules for SUPER GT drivers and personnel.
In the GT300 class, the restrictions are set to force a number of drivers to miss the opener, including Nicki Thiim (D'station Aston Martin), Christopher Mies (Hitotsuyama Audi), Andre Couto and Dennis Lind (both JLOC Lamborghini), all of whom were absent for the test.
While JLOC has designated third drivers for each car ready to step in, D'station and Hitotsuyama ran with only one driver each at Fuji - Tomonobu Fujii and Shintaro Kawabata respectively - and it remains to be seen who would be nominated to join them.
The Panther arto Team Thailand Lexus squad meanwhile missed the test entirely due to the travel restrictions, and is likewise in danger of not being able to race at Fuji this month. The other GT300 car absent from the test, the R'Qs Motor Sports Mercedes, is understood to have not been present because of financial problems.