Froome, 32, said he had done nothing wrong and explained in a statement that he had followed medical advice and taken an increased dosage of asthma medication without exceeding the permitted limits.
Cycling's world governing body, the UCI, said in a statement it had notified Froome on 20 September of an 'Adverse Analytical Finding" from a sample collected after Stage 18 of the race on 7 September.
The sample had double the permissible limit of Salbutamol, which is permitted as a legal asthma drug by the World Anti-Doping Agency.
"It is well known that I have asthma and I know exactly what the rules are," the rider said in a statement issued by Team Sky.
"I use an inhaler to manage my symptoms (always within the permissible limits) and I know for sure that I will be tested every day I wear the race leader's jersey."
Froome said his asthma had worsened at the Vuelta so he followed the team doctor's advice and increased his Salbutamol dosage.
"As always, I took the greatest care to ensure that I did not use more than the permissible dose," he said.
"I take my leadership position in my sport very seriously. The UCI is absolutely right to examine test results and, together with the team, I will provide whatever information it requires."
The UCI said analysis of the B sample had confirmed the results of the rider’s A sample and proceedings were being conducted in line with its anti-doping rules.
"As a matter of principle, and whilst not required by the World Anti-Doping Code, the UCI systematically reports potential anti-doping rule violations via its website when a mandatory provisional suspension applies," it added.
"The presence of a Specified Substance such as Salbutamol in a sample does not result in the imposition of such mandatory provisional suspension against the rider."
Sky said Froome had suffered from asthma since childhood and takes Salbutamol, a common medication, to prevent and ease symptoms brought on by exercise.
Salbutamol is permitted by WADA rules, without the need for a therapeutic use exemption, when inhaled up to a limit of 1,600 micrograms over a period of 24 hours and no more than 800 over 12 hours.
Sky said analysis of Froome's sample showed the presence of Salbutamol at a concentration of 2,000 nanograms per millilitre (ng/ml), compared with the WADA threshold of 1,000ng/ml.
It said none of the 20 other urine tests taken by the rider had required any further explanation.