Rainey said it was common for BART officers to do searches as part of follow-up investigations to recover stolen property.
"I'm very confident in the training that our personnel have received to make sure they're prepared to deal with these types of encounters and situations," Rainey said. "Because you never know what's on the other side of the door."
Smith, 42, of San Ramon was in charge of the BART police detective unit. He is survived by his wife, also a BART officer, a 6-year-old daughter and two brothers who are also in law enforcement in the San Francisco Bay Area, Rainey said.
"Tommy was a great law enforcement officer, but an even better son, brother, husband, father and friend," Rainey said. "He touched many lives in a positive way both professionally and personally and he will be sorely missed."
On Wednesday afternoon, Smith's family spoke publicly to reporters for the first time.
"If you're lucky to find the love of your life, you hold onto it. I did," Smith's wife, Kellie, told KPIX-TV in an interview at the family's East Bay home. "I cherished every moment we had."
She added: "Tommy will always be in my heart, and I'll love him forever. He was the love of my life."
Kellie, who is a canine patrol officer with BART Police, was joined in the interview by Tom Smith's brothers Patrick and Ed and his brother-in-law Todd Shaheen. Patrick Smith is a field training officer with the Newark, Calif., Police Department, while Ed Smith works for the Alameda County Sheriff's Department.
Patrick said his heart also goes out to the officer who accidentally shot his younger brother.
"We're going to mourn the loss of our brother. We'll never forget him," he said. "But there's someone else in another family that's affected by this, too, and I feel sorry for them."
After Tom Smith was shot, he was taken to Eden Medical Center in Castro Valley, where he died. Television reports on Tuesday showed lines of officers outside the hospital saluting as their fallen comrade's body, covered with a large American flag, was loaded into a coroner's van.
BART police have been the center of other controversies. On New Year's Day 2009, Oscar Grant III, an unarmed black passenger, was shot and killed at the Fruitvale station after reports of a fight.
Officer Johannes Mehserle, who is white, was convicted of involuntary manslaughter and sentenced to two years minus time served.
An independent auditor said last month that BART police have made significant progress in meeting reforms instituted after Grant's death, including increased officer training about bias and other issues, along with better reporting about incidents involving use of force.