Deposition costs are covered as follows:

• Expenses incurred in the taking of fact witness depositions (notary fees, interpreters, transcripts, etc.) are paid by the Department of Justice (DOJ), regardless of which party requested the deposition.
• The costs of attendance of fact witnesses at the deposition for either party are paid by the DOJ.
• The costs of attendance of expert witnesses for the defense at the deposition are paid under the Criminal Justice Act (CJA).
• If the government is the requesting party, expenses incident to attendance of both counsel and defendant at the deposition are paid by the DOJ. If depositions are at the instance of the defense, these expenses are paid by CJA. [Guide, Vol. 7, § 320.40.20(d)]

[Guide, Vol. 7, § 320.40.20] [Federal Rule of Criminal Procedure 15] [Federal Rule of Criminal Procedure 17]

In 28 U.S.C. § 2254 and 28 U.S.C. § 2255 habeas corpus cases, the court may order the state or the government to pay the "expenses of travel and subsistence and fees of counsel" to attend the taking of a deposition at the request of the state or government. [Guide, Vol. 7, § 320.40.30]

See Rules Governing §§ 2254 and 2255 Cases in U.S. District Courts, Rules 6.