It follows similar comments by FBI director James Comey who said in a speech on Thursday that the hack used to unlock the encrypted phone works on a "narrow slice" of devices.
Apple attorneys said that the company is "confident" that the security weakness that the government alleges to have found will have a "short shelf life." The attorneys were keen to stress that they had no evidence what the flaw was, but argued that the normal product development would see that a fix for the flaw would be implemented down the line.
The FBI's hack in the San Bernardino case would not help agents access a newer iPhone 5s used by a drug dealer in New York, where Apple faces a similar case against the government.
The government is demanding that Apple helps to extract data on Jun Feng, who last year pleaded guilty to numerous drug charges.
Apple won the case in February after the New York-based magistrate said that the government's use of a 227-year-old law would not apply in the case, because lawmakers have not yet adopted legislation that would achieve the result sought by the government.
The government appealed the case Friday, saying that it "continues to require Apple's assistance in accessing the data" on the phone.
But Apple attorneys said that there was a "healthy amount of skepticism" that the government doesn't have the ability to use some other method of getting into Feng's phone.
The company said it will be asking the government why it doesn't believe it can access the phone, and whether or not it has sought the help from external forensic firms.
Apple's response is expected to be filed on Thursday.