That's almost $2 million more than the federal utility paid former CEO Tom Kilgore, who retired at the end of 2012, during his last year with the agency. He made just under $4.03 million.
The Chattanooga Times Free Press cited the TVA's year-end financial report, which was filed Monday with the U.S. Securities and Exchange Commission.
The utility said that even with the increase Johnson's pay is still below the industry average.
TVA is the nation's largest public utility, supplying power to about 9 million people in Tennessee, Alabama, Mississippi, Kentucky, Georgia, North Carolina and Virginia.
Most of his salary came from performance incentives of nearly $2.6 million and deferred compensation payments of $2.06 million. His base salary for nine months of work was $712,500.
Other top executives at TVA saw a decline in pay.
Chief financial officer, John Thomas, received $2.1 million in 2013, or 3.3 percent less than in 2012. TVA'schief counsel, Ralph Rogers, received 25 percent less than the previous year with pay of $1.9 million.
The utility ended fiscal 2013 with $271 million in net income on $11 billion in operating revenues. Although the utility has a decline in sales, it said record levels of hydroelectric generation helped offset increased fuel costs.
"TVA reported solid financial results in 2013 despite lower sales and revenues," Johnson said in a statement.
"We experienced lower demand for power during the year due to the shutdown of a major customer facility, a slow-growing economy and adoption of energy conservation by customers," he said. "We expect to see low growth in power demand into the next decade, and we are committed to living within our means to keep rates low for our customers and the people of the Tennessee Valley."