Police Chief Charles McClelland also asked the community to "reserve judgment" on the officer and his actions at the Healing Hands group home for the mentally ill, and sought to reassure the public that all of the city's officers are trained to deal with people with mental problems.
It's the second time Marin has killed a suspect while on duty. In 2009, investigators said Marin came upon a man stabbing his neighbour to death at an apartment complex and fired when the suspect refused to drop the knife, according to the Houston Chronicle.
Community and civil rights groups say the incident is another example of problems the police department has with using excessive force.
Officer Matthew Marin shot 45-year-old Brian Claunch after responding to a call that the man, who reportedly lost two limbs in a train accident, was causing a disturbance.
Police have said Claunch cornered and threatened Marin, who reportedly told investigators he didn't know the object in Claunch's hand was a pen.
John Garcia, who owns the group home, told reporters over the weekend that Claunch liked to draw.
Police spokeswoman Jodi Silva said she didn't know if FBI assistance in officer-involved shootings was rare, but said "it's the step we're taking at this point."
The Greater Houston Coalition for Justice, a group that includes 16 local and national civil rights organizations, suggested Claunch's death was part of a bigger problem at the police department.
"The deeper problem is a failure to discipline for excessive force, especially in the area of shootings," said Randall Kallinen, a member of the group and local a civil rights attorney.
Kallinen said he would like the shooting to spark a change in the police department regarding discipline and training of officers.
Marin, a five-year veteran of the department, has been placed on three-day administrative leave. That is standard department procedure for all officer-involved shootings, and Silva said no unusual measures were being taken that would prevent Marin from returning to duty this week.
Marin and a partner arrived at the group home around 2:30 a.m. responding to a disturbance call made by the group's caretaker. Police have not elaborated on the nature of the disturbance before they arrived.
Once inside the home, the department said in a separate statement released Monday, they found an agitated Claunch threatening to kill the officers and other residents. While yelling at the officers, Claunch "waved a shiny object in his hand in their direction," according to the statement.
Police say Claunch refused an officer's direction to drop what turned out to be a ballpoint pen.
"As the suspect backed one of the officers into a corner, he attempted to stab the officer with the object," the statement said. "Officer Marin, fearing for his partner's life, and his own safety, discharged his duty weapon one time, striking the suspect."
Estella Olguin, a spokeswoman for the Harris County Guardianship Program, said Claunch had been a ward of the country since 2003 and had lived at the home since March.
Garcia said Claunch had lost his right leg to just above the knee and his entire right arm when he was hit by a train, according to the Houston Chronicle. He said Claunch was schizophrenic.
Relatives of Claunch could not be found Monday. Public records show Claunch had brushes with the law multiple times over the last 20 years, including a 2006 arrest for trespassing at a shelter. His record also includes drug convictions.