Student loan borrowers' complaints to a federal watchdog suggest that some are having more problems dealing with their lenders or loan servicers than they are with making repayments.

The finding emerges from the latest annual report by the Consumer Financial Protection Bureau's student loan ombudsman, based on analysis of borrower complaints filed with the watchdog from September 1, 2016, through August 31, 2017.

Difficulties include gaining access to federal programs, such as income-driven repayments and the ability to consolidate older federal loans and getting access to lower interest rates that some private companies advertise as a reward for paying on time.

The report cautions that the prevalence of the issues that the borrowers reported may not be representative of the entire U.S. student loan market.

The total number of federal student loan complaints filed with the consumer agency was 12,900. The total comes from the first full year of data since the consumer bureau began handling federal student loan complaints in late February 2016. The watchdog handled approximately 3,900 federal student loan complaints between March 1, 2016, and August 31, 2016.

The company most complained about: Navient

As in 2016, student-loan servicing giant Navient was the company that was most frequently the subject of borrower complaints. The Delaware company is one of the largest handlers of both federal and private student loans.

Navient services 28% of all federal student loans and 29% of private education loans that are in repayment, the company said in a March 2017 analysis of borrower complaints submitted to the consumer watchdog.

The consumer bureau in January filed a federal lawsuit that accused Navient of failing borrowers by providing incorrect payment information, processing payments incorrectly and failing to act when borrowers complained.

The attorneys general of Illinois and Washington made similar accusations in separate lawsuits filed in January. Those cases also allege Navient sold subprime private student loans that saddled borrowers with high rates and fees. Pennsylvania's attorney general filed a similar complaint against the company this month.

The cases are pending, and Navient has denied the allegations. The company has argued that the consumer watchdog was not authorized to sue because it had not issued rules that cover any of the alleged practices.

Companies with the most federal student loan complaints, ranked by volume

Navient: 6,274, or 61%

AES/PHEAA: 1,517, or 15%

Nelnet: 629, or 6%

Great Lakes: 340, or 3%

ACS Education Services: 192, or 2%

Percentages are based on 10,236 complaints

Companies with the most private student loan complaints, ranked by volume

Navient: 4,030, or 61%

AES/PHEAA: 414, or 6%

SLM Corp.: 362, or 5%

Wells Fargo: 303, or 5%

Discover Bank: 189, or 3%

Percentages are based on 6,642 complaints

Complaints from federal student loan borrowers

Federal student loan borrowers continued to complain of difficulty gaining access to federal programs, such as income-driven repayments and the ability to consolidate older federal loans and become eligible for repayment savings, the ombudsman report said.

Federal student loan issues reported by borrowers

Dealing with lender or loan servicer: 7,259, or 71%

Struggling to repay your loan: 2,821, or 28%

Problem with credit report or credit score: 155, or 2%

Getting a loan: 1

Percentages are based on 10,236 complaints

Complaints from private student loan borrowers

Private student loan borrowers complain about difficulties obtaining monthly repayment levels they can afford and also say it is hard to gain access to lower interest rates some companies advertise for on-time repayments, the report said.

Private student loan issues reported by borrowers

Dealing with lender or loan servicer: 4,059, or 61%

Struggling to repay your loan: 2,318, or 35%

Getting a loan: 202, or 3%

Problem with credit report or credit score: 63, or 1%

Percentages are based on 6,642 complaints

More:Trump to grant student loan servicing work to just one company

3 things your student loan servicer might not tell you

Student loan borrowers owe more, need longer to repay in full

Follow USA TODAY reporter Kevin McCoy on Twitter: @kmccoynyc