There are several Votive Masses and Commemorations in the 1962 Missal for related intentions ('For the Church', 'Against Persecutors', 'For Peace' and the like). The Collect of one of them was enriched with an indulgence in 1934, for use as a prayer on its own. The indulgence was abolished in 1968 but we can still say the prayer.
Graciously hear the prayers of Thy Church, we beseech Thee, O Lord: that her enemies and all heresies be brought to nought, and that she may serve Thee in perfect security and freedom. Through Christ our Lord. Amen.
Ecclésiae tuae, quǽsumus, Dómine, preces placátus admítte: ut, destrúctis adversitátibus et erróribus univérsis, secúra tibi sérviat libertáte. Per Christum Dóminium nostrum. Amen.
Translation from The Raccolta, the official handbook of indulgenced prayers.
The Raccolta also includes this short prayer, taken from the Roman Ritual:
That Thou wouldst vouchsafe to bring low the enemies of holy Church, we beseech Thee to hear us.
Ut inimicos sanctae Ecclesiae humiliare digneris, te rogamus, audi nos.
A longer prayer, which was also granted an indulgence in 1934, was issued as a Prayer Card by the Catholic Truth Society with an imprimatur from Cardinal Godfrey in 1962:
Almighty, everlasting God, look with compassion on all those who suffer persecution for justice’ sake. Grant them grace to carry their cross with patience in the name of Thy beloved Son, our Lord and Saviour Jesus Christ. Let the chalice pass from them is such by Thy holy Will: yet, in all things, may Thy Will be done. Grant to those who persecute, light to see the truth, and the grace of mercy and forgiveness, for they know not what they do. Mary, Mother of Jesus, Comfort of the Afflicted, help thy children in their time of bitter trial. O Lord our God, by the sign of Thy holy cross deliver us from our enemies.
The Prayers After Low Mass were instituted by Pope Pius IX in 1859 against the threat to the Papal States, and the following prayer implores 'liberty and exaltation of the Church'. (The reference to the 'conversion of sinners', and the Prayer to St Michael which now follows this prayer, was added by Pope Leo XIII in 1886.):
O God, our refuge and our strength, look down in mercy on thy people who cry to thee; and by the intercession of the glorious and immaculate Virgin Mary, Mother of God, of St Joseph her spouse, of thy blessed apostles Peter and Paul, and of all the saints, in mercy and goodness hear our prayers for the conversion of sinners, and for the liberty and exaltation of our holy Mother the Church. Through the same Christ our Lord. Amen.
Deus, refúgium nostrum et virtus, pópulum ad te clamántem propítius réspice; et intercedénte gloriósa et immaculáta Virgine Dei Genetríce María, cum beáto Ioseph, eius Sponso, ac beátis Apóstolis tuis Petro et Paulo, et ómnibus Sanctis, quas pro conversióne peccatórum, pro libertáte et exaltatióne sanctæ Matris Ecclésiæ, preces effúndimus, miséricors et benígnus exáudi. Per eúndem Christum Dóminum nostrum. Amen.
The Manual of Prayer for England and Wales has prayers for a procession, with the Great Litany, 'In time of war against enemies of Holy Church', which concludes with these prayers:
Grant unto thy Church, we beseech Thee, O merciful God, that She, being gathered together by the Holy Ghost, may be in no wise troubled by attack from her foes.
O God, who by sin art offended and by penance pacified, mercifully regard the prayers of thy people making supplication unto Thee, and turn away the scourges of thine anger which we deserve for our sins.
Almighty and Everlasting God, in whose hand are the power and the government of every realm: look down upon and help the Christian people that the heathen nations who trust in the fierceness of their own might may be crushed by the power of thine arm. Through our Lord Jesus Christ, thy Son, who liveth and reigneth with Thee in the unity of the Holy Ghost, God, world without end. Amen
Finally, here is a longer prayer from the Raccolta:
Prayer to Our Lady Help of Christians.
Virgin most powerful, loving helper of the Christian people, how great thanks do we not owe thee for the assistance thou didst give our fathers, who, when they were threatened by the Turkish infidels, invoked thy maternal help by the devout recitation of thy Rosary! From heaven thou didst see their deadly peril; thou didst hear their voices imploring thy compassion; and their humble prayers, enjoined by the great Pope, Saint Pius the Fifth, were acceptable unto thee, and thou camest quickly to deliver them. Grant, dear Mother, that in like manner the prolonged sighs of the holy Bride of Christ in these our days may come to thy throne and engage thy pity; do thou, moved anew to compassion for her, rise once again to deliver her from the many foes who encompass her on every side.
Even now from the four quarters of the earth there arises to thy throne that lovéd prayer, to win thy mercy in these troublous times even as of old. Unhappily our sins hinder, or at least retard, its effect. Wherefore, dear Mother, obtain for us true sorrow for our sins and a firm resolution to face death itself rather than return to our former iniquities; we are sore distressed that, through our fault, thy help, of which we stand in such extreme need, should be denied or come too late.
Rise, then, O Mary, incline thyself to hear the prayers of the whole Catholic world, and beat flat to the ground the pride of those wretched men, who in their insolence blaspheme Almighty God and would destroy His Church, against which, according to the infallible words of Christ, the gates of hell shall never prevail. Let it be seen once more that when thou dost arise to protect the Church, her victory is sure. Amen.
SC Ind 1891; SP Ap 1935