City chief financial officer Mike Richardson said the R91-million shortfall, which had to be siphoned from various council departments, would affect their budgets.
Housing mayoral committee member Dan Plato said the money used for xenophobia relief measures were needed for other projects.
"We need to tell citizens out there that we can't afford to spend money like this."
In a report to the city's mayoral committee on Tuesday, Johan Steyl of the finance department said the city submitted reimbursement claims of R70,7-million, R5,6-million and R32-million to the the province and national government.
"The claims related to actual costs incurred," Steyl said.
The claims were submitted in June, August and September.
Since then, the city has racked up a further R1,9-million in xenophobia-related costs.
Meanwhile, the department of provincial and local government said in a letter to the provincial disaster management centre that the National Treasury had approved an amount of R12,8-million for the provincial departments and R17,3-million for the City of Cape Town.
Steyl said it was not clear whether this amount would cover all claims, including costs incurred after the submission of the last invoices, or only a part of the claims.
The city was then told by the National Treasury that the allocation was evaluated on the basis of whether the claim was reasonable and whether the expenditure was deemed appropriate.
Steyl said the city did not make provision in its budgets for the xenophobic attacks, which erupted without warning in May.
Relief measures, including shelter and support for the thousands of people who were displaced and housed in safety sites, put the budgets of the city's departments "under considerable strain".
- Cape Times