"Clearly we are not in control right now," he testified, warning that not enough Americans are wearing masks or social distancing.
During the hearing, he said about half of all new cases come from four states.
Earlier, the New York governor said nearly half of all Americans must self-quarantine if they visit the state.
On Tuesday, cases rose by more than 40,000 in one day for the fourth time in the past five days.
The surge - which is occurring particularly strongly in southern and western states - has forced at least 16 states to pause or reverse their reopening plans, according to CNN. Florida, Arizona, Texas and California are the four states referenced by Dr Fauci as being most heavily hit currently.
For some the new measures come over a month after they first began to reopen their economies.
Also on Tuesday, New York Governor Andrew Cuomo expanded the number of Americans who are required to self-quarantine for 14 days if they visit the state. There are now 16 states on the list.
The newly added states are California, Georgia, Iowa, Idaho, Louisiana, Mississippi, Nevada and Tennessee.
They join Alabama, Arkansas, Arizona, Florida, North Carolina, South Carolina, Texas and Utah.
All together, the order affects 48% all US residents, according to a USA Today analysis.