More than a third of these cases had to be prioritised due to the person involved experiencing "severe financial difficulties", the FOS said. Common complaints included customers having trouble meeting payments, including cases where charges had been added to the mortgage balance.
Lenders are required to treat customers sympathetically and make "reasonable attempts" to agree a repayment plan.
But this means a lender relies on customers communicating openly with them and providing information when it is requested, the ombudsman said.
The watchdog is seeing many complaints where people put off asking for help and missed too many payments to be able to sort their situation out.
The FOS, which resolves disputes between consumers and financial institutions, said it had also seen a small number of instances surrounding how lenders handled cases which led to a repossession, although it emphasised that it cannot overturn a court's decision.
More than a million home owners had their mortgage rates put up in May by lenders, who blamed the weak economy and the increased cost of funding a mortgage.
Lenders have also been steadily increasing their mortgage rates for new borrowers in recent months, and those with a smaller deposit are expected to have a particularly tough time trying to find a deal in the coming months as lenders tighten their criteria and borrowing becomes more expensive.
The above payments are for illustration purposes only. You need to consider any insurance payments that also need to be made. Please note that any changes to your mortgage, for example, as a result of changes to the Bank of England base rate (variable rates only) or any overpayments you make, may affect your monthly payments. * For interest only mortgages you need to add on the cost of repaying the capital with a repayment vehicle such as an ISA or endowment policy. Loan to value (LTV) restrictions apply.
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