Terry Childs, 43, will plead not guilty in court today, his lawyer told ABCNews.com.
Childs, an employee of the city's Department of Technology, was arrested Sunday and charged with four counts of computer network tampering.
"He was able to prevent other authorized users from being able to access the system, and at same time, put in place devices that gave him access to areas of the network which he was not authorized to access," said Erica Derryck, spokeswoman for the San Francisco district attorney's office.
Childs worked as a network administrator for five years and was instrumental in designing the router system for the city's FiberWAN (wide-area network), according to his lawyer, public defender Mark Jacobs.
The network on which he worked reportedly stored 60 percent of all municipal data, including the city's 311 system, employee e-mail and law enforcement records.
San Francisco Mayor Gavin Newsom told reporters Tuesday that Childs was a "rogue employee that got a bit maniacal and full of himself.
"There's nothing to be alarmed about, save the inability to get into the system and tweak the system," Newsom said. "Nothing dramatic has changed in terms of our ability to govern the city."
Jacobs said it was "important to follow the mayor's lead and recognize that business is going on as usual. There is no problem with the system; no tampering with the system; no hijacking of the system. There is an accusation that he locked everyone out, but things seem to be running fine."
Jacobs added there was no indication that any information had been stolen or compromised.
He chalked up the arrest to a "misunderstanding between [Childs] and a supervisor that does not affect anything."
Prosecutors would not release the full criminal complaint to the public, nor would they disclose what they believe was Childs' motive for creating a password that would block other administrators from accessing the network.
The San Francisco Chronicle reported that Childs allegedly had a dispute with his boss that led him to hack the system.
According to the Chronicle, Childs was ordered to leave work July 9 for alleged insubordination. While in jail, he remains on the city payroll, reportedly earning $127,735 a year.
Childs was convicted of aggravated robbery and burglary in 1982, the Chronicle also reported.
Jacobs called his client's $5 million bail "ridiculous and uncalled for.
"Murderers get $1 million bail and this guy didn't kill anyone. It doesn't make any sense," he said.
Derryck defended the high bail and said Childs' alleged actions constituted a "threat to public safety, and that bail was appropriate."
Despite Jacobs's defense of Childs in the media, the public defender's boss told ABCNews.com that their office would soon stop defending the network technician.
"Our office is declaring a conflict of interest. At the hearing, the court will appoint a private attorney," said Teresa Caffese, the chief attorney for the San Francisco Public Defender.
"We're part of the city and county of San Francisco, and we believe there may be a conflict," she said.
Newsom said the city was working to restore access to the network, but a complete rebuild of the network could take up to two months.
"Worst-case -- this is the absolute worst-case -- it's six to eight weeks they can rebuild the entire system and shut this one down," Newsom told reporters Tuesday. More technology news | Houston blogs | Houston headlines on Twitter | RSS feeds