The US energy department is the latest agency to confirm it has been breached in what is being described as the worst-ever hack on the US government.
The department is responsible for managing US nuclear weapons, but said the arsenal's security had not been compromised.
Tech giant Microsoft also said on Thursday that it had found malicious software in its systems.
Many suspect the Russian government is responsible. It has denied any role.
The US treasury and commerce departments are among the other targets of the sophisticated, months-long breach, which was first acknowledged by officials on Sunday.
President Donald Trump is yet to comment on the cyber-attacks.
Meanwhile, US President-elect Joe Biden has vowed to make cyber-security a "top priority" of his administration.
"We need to disrupt and deter our adversaries from undertaking significant cyber-attacks in the first place," he said. "We will do that by, among other things, imposing substantial costs on those responsible for such malicious attacks, including in coordination with our allies and partners."
America's top cyber agency, the Cybersecurity and Infrastructure Agency (Cisa), gave a stark warning on Thursday, saying that addressing the intrusion would be "highly complex and challenging".
It said "critical infrastructure" had been damaged, federal agencies and private sector companies compromised, and that the damage posed a "grave threat".
The hack began in at least March 2020, and those responsible had "demonstrated patience, operational security, and complex tradecraft", the Cisa said.
The agency did not identify what information had been stolen or exposed.
Addressing the attack on the energy department, spokeswoman Shaylyn Hynes confirmed that it was responding to a cyber breach but said "the malware has been isolated to business networks only".
She said security functions at the National Nuclear Security Administration (NNSA), which oversees US nuclear weapons, had not been affected.
The list of who was hacked is already long - and it is going to get longer. These are still early, and quite frantic, days in the investigation as government departments, companies and organisations race to see if they have a backdoor in their systems and what might have been stolen through it over a period of months.
The scale is potentially huge, but the truth is no one is quite sure of the impact yet. So far, this looks to have been classic espionage - the targeted theft of information. There is not much sign yet that the hackers were planning to disrupt systems or carry out real world damage, although that could still emerge.
That also makes it trickier for the US to respond - after all, espionage is something it also carries out regularly. The problem is that in this case US defences were not good enough to spot and stop those responsible. (BBC)