Supposedly, after problems were found with the 10mm the FBI were using, they were quietly issued 9mm pistols
I think standard FBI issue from the late 80s to 1998 was the Sig Sauer P226 9mm.
http://www.fortunecity.com/tattooine/leiber/50/DGAAAFED.html
Federal Bureau of Investigation (FBI)
The FBI issued 9×29mmR (.38 Special) Colt Official Police and 9×29mmR (.38 Special) S&W Model 13 Military & Police revolvers in the 1980s. Authorised privately-purchased weapons included the 9×33mmR (.357 Magnum) S&W Model 19 Combat Magnum revolver and 11.43×23mm (.45 ACP) SIG-Sauer P220-1 pistol. This situation was finally seen as no longer adequate, and some 1,500 9×19mm SIG-Sauer P226 and 1,000 9×19mm S&W Model 5946 pistols were purchased in 1988, which most field agents never got, however. In 1991, the Bureau received at least 9,500 copies of the 10×25mm S&W Model 1076, which was especially designed for the FBI (as seen in "Twin Peaks"). It was issued with four 9-round magazines, two 11-round magazines and one 15-round magazine per agent. However, the gun turned out to be a complete failure. All were returned to the factory. Thus, some 15,000 9×19mm SIG-Sauer pistols were purchased over the course of the 1990s, most of them P226s. In 1993, the more compact 9×19mm SIG-Sauer P228 was adopted. Agents with very small hands, especially women, could opt for the slimline 9×19mm SIG-Sauer P225. Since January 1998, all new agents are trained on the 10×21mm (.40 S&W) Glock 22 pistol, with the smaller 10×21mm (.40 S&W) Glock 23 for those who prefer it. The ultra-compact 10×21mm (.40 S&W) Glock 27 is authorised as concealed backup. Older agents continue to field their SIG-Sauer pistols, if they wish, and even new agents can switch to the 9×19mm guns if they qualify with them. Several small revolvers are authorised for undercover agents, including the 9×29mmR (.38 Special) S&W Model 10 Military & Police (with 2" barrel), 9×29mmR (.38 Special) S&W Model 38 Bodyguard Airweight (with 2" barrel), 9×29mmR (.38 Special) S&W Model 60 Chief's Special Stainless (with 2" barrel) and 9×33mmR (.357 Magnum) S&W Model 19 Combat Magnum (with 2.5" barrel).
Since 1989, the FBI issued the 9×19mm H&K MP5SFA2 (and MP5SFA3) semi-automatic carbine to field agents. These are identical to the MP5A4 and MP5A5 submachine guns respectively, except for the fact that they are only capable of single shots. Beginning in 1994, they were replaced by the 10×25mm H&K MP5/10A2 submachine gun (offering single shots and 2-round bursts only). In rural areas, semi-automatic 5.56×45mm carbines and rifles such as the Colt CAR-15A2 Model 6520 are used. Only SWAT-qualified agents can field full-automatic weapons. The standard shotgun is the 18.5×70mmR SGT Tactical Response Model 90102 FBI, a modified Remington Model 870 with tactical light and spare rounds holder.