I am an indian citizen employed in the usa. My status for 2005 was :

Jan-Oct : F1/OPT
Oct-Dec : H1

My employer deducted social security and medicare taxes from oct-dec when I was on h1.
While filing taxes, my tax consultant told me that since social security and medicare are charged per calendar year, and I was on f1 status at the start of the calendar year, I can ask for a refund of the amt charged between oct-dec.
I want to double check this.

Thanks

The exemption from social security tax applies only while you are in F-1 status. It does not apply when you are H1-B. See the following from the IRS website:

F-visas, J-visas, M-visas, Q-visas. Nonresident alien students, scholars, professors, teachers, trainees, researchers, and other aliens temporarily present in the United States in F-1,J-1,M-1, or Q-1/Q-2 nonimmigrant status are exempt from Social Security / Medicare Taxes on wages paid to them for services performed within the United States as long as such services are allowed by the United States Citizenship and Immigration Services (USCIS) for these nonimmigrant statuses, and such services are performed to carry out the purposes for which they were admitted into the United States.
Exempt Employment includes:
On-campus student employment up to 20 hours a week (40 hrs during summer vacations)
Off-campus student employment allowed by USCIS
Practical Training student employment on or off campus
On-campus employment as professor, teacher or researcher
Limitations on exemption:
The exemption does not apply to spouses and children in F-2, J-2, M-2, or Q-3 nonimmigrant status.
The exemption does not apply to employment not allowed by USCIS or to employment not closely connected to the purpose for which they were admitted into the United States.
The exemption does not apply to nonimmigrants in F-1,J-1,M-1,or Q-1/Q-2 status who change nonimmigrant status to a status which is not exempt or to a special protected status. The exemption does not apply to nonimmigrants in F-1,J-1,M-1, or Q-1/Q-2 status who become resident aliens for tax purposes.

TaxSearcher says it all quite nicely.

What about the following similar situation:

June08 - Dec08 (calendar year 2008, F-1 visa holder), by mistake my employer withheld SS and Medicare.

Jan 09 - June 09 - still F-1, no SS and Medicare withheld

June 09 - present - changed to H-1 visa status, SS and Medicare withheld, plus paid back SS and Medicare taxes retroactively from Jan 09 - June 09, since changed visa status in that calendar year.

Now I want to get my SS and Medicare taxes from June08 - Dec 08, the calendar year that I was on F-1 visa status, but my employer says I do not qualify. Is he right?

You DO qualify for a refund of the FICA (Social Security and Medicare) taxes withheld from June 2008 through December 2008. Your employer CAN still get this refund processed, and should be willing to do so because, for every dollar you get refunded, he gets a dollar as well.

You can find the regulatory citation in IRS Pub 519, pages 49-52, which can be downloaded from Internal Revenue Service (http://www.irs.gov).

If your employer does NOT want to cooperate, try to get a refusal letter on company letterhead citing the amount of FICA taxes withheld for the period in question.

You would then need to submit the letter, plus other support documentation, along with Form 843 and 8316, to the IRS to request the refund of the FICA taxes yourself.

The letter DOES expedite the process, but is NOT absolutely essential to getting the FICA taxes back.

What is social security and medicare refunds do they pay me

What was your visa status when the FICA (Social Security and Medicare) taxes were withheld?