"We are seeing a limited number of instances where there have been efforts through cyber intrusions to get into the online presence of various state election agencies. And, one or two of them have been successful, others have not," Johnson said at a Senate Homeland Security Committee hearing.
The issue of the integrity of US elections has been a prominent one on the presidential campaign trail, with Republican presidential nominee Donald Trump and Democratic Sen. Harry Reid each raising concerns about possible rigging of the results. Both Trump and his Democratic rival, Hillary Clinton, said at Monday's debate that they would respect the election results.
Asked by Sen. Jon Tester, D-Montana, whether hackers are seeking to change votes, Johnson said: "What we are seeing are efforts to get into voter registration rolls, the identity of registered voters, things of that nature, not to change a ballot count."
Johnson said the matter was still an active investigation and that the source of the intrusions hadn't been concluded.
US officials briefed on the investigation have told CNN that an intrusion in an Illinois voter registration database and an attempted breach in Arizona are believed to be the work of hackers working for Russian spy agencies. US officials say there's strong evidence that Russian government hackers are behind a series other cyber-attacks against the Democratic National Committee and other affiliated political organizations.
Johnson, FBI Director James Comey and Nick Rasmussen, director of the National Counterterrorism Center, on a variety issues during the hearing, ranging from the perceived missteps that failed to prevent recent domestic terrorist attacks to the Hillary Clinton email investigation.
Lawmakers used the hearing to press Comey on the FBI's handling of suspects in recent domestic attacks, including those behind the Orlando mass shooting and the bombings in New York and New Jersey. The FBI had done preliminary investigations prior to the attacks on both suspects but closed the files on both men after not finding enough evidence to continue.
"I'm not here to say the FBI is terrible because it missed these things, but I'm also troubled that the FBI is unwilling to even admit they've made some mistakes," Sen. Rand Paul, R-Kentucky, said.
Comey said the FBI will review the case of the alleged New York bomber Ahmad Rahami to see if anything was mishandled.
"We will go back and scrub our prior contact with that matter very, very carefully -- and maybe the inspector general will as well, which would be great as well -- and if there is learning, we will learn from it," he said.
Republicans on the committee renewed their criticism of the FBI for recommending no charges be brought in the Clinton probe. Comey said the FBI didn't find evidence to bring charges for possible obstruction of justice.
Comey spoke of the increased threat of domestic attacks as the US bombing campaign against ISIS prompts foreign fighters to return home.
"The so called (ISIS) caliphate will be crushed -- the challenge will be through the fingers of that crush are going to come hundreds of very, very dangerous people," Comey said. "They will not all die on the battlefield in Syria and Iraq. There will be a terrorist diaspora sometime in the next two to five years like we have never seen before."